From 63901f6940922b3770834c8e31d46c5815ed2421 Mon Sep 17 00:00:00 2001 From: Alejandra Gonzalez-Beltran Date: Tue, 2 Jun 2015 16:04:35 +0100 Subject: [PATCH] updating workflows in investigation and assay files --- isa-tab/a_assay_soapdenovo2.txt | 2 +- isa-tab/i_Investigation.txt | 100 +------------------------------- 2 files changed, 2 insertions(+), 100 deletions(-) diff --git a/isa-tab/a_assay_soapdenovo2.txt b/isa-tab/a_assay_soapdenovo2.txt index af7925d..757a3b8 100644 --- a/isa-tab/a_assay_soapdenovo2.txt +++ b/isa-tab/a_assay_soapdenovo2.txt @@ -1 +1 @@ -Sample Name Protocol REF Extract Name Protocol REF Parameter Value[library source] Parameter Value[library strategy] Parameter Value[library selection] Parameter Value[library layout] Protocol REF Parameter Value[sequencing instrument] Assay Name Comment[Export] Raw Data File Protocol REF "Parameter Value[sequence assembly algorithm,http://purl.obolibrary.org/obo/OBI_0001522,OBI]" Term Source REF Term Accession Number Parameter Value[workflow engine] Term Source REF Term Accession Number Parameter Value[workflow execution history] Term Source REF Term Accession Number Data Transformation Name Derived Data File Comment[Derived Data File information] Protocol REF Data Transformation Name Derived Data File Factor Value[sequence assembly algorithm] Term Source REF Term Accession Number Factor Value[genome size] Term Source REF Term Accession Number assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz soapdenovo2-sequence assembly SOAPdenovo version 2 Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz soapdenovo1-sequence assembly SOAPdenovo version 1 Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz ALLPATHS-LG-sequence assembly ALLPATHS-LG Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 yes ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size # S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size \ No newline at end of file +Sample Name Protocol REF Extract Name Protocol REF Parameter Value[library source] Parameter Value[library strategy] Parameter Value[library selection] Parameter Value[library layout] Protocol REF Parameter Value[sequencing instrument] Assay Name Comment[Export] Raw Data File Protocol REF "Parameter Value[sequence assembly algorithm,http://purl.obolibrary.org/obo/OBI_0001522,OBI]" Term Source REF Term Accession Number Parameter Value[workflow engine] Term Source REF Term Accession Number Parameter Value[workflow execution history] Term Source REF Term Accession Number Data Transformation Name Derived Data File Comment[Derived Data File information] Protocol REF Data Transformation Name Derived Data File Factor Value[sequence assembly algorithm] Term Source REF Term Accession Number Factor Value[genome size] Term Source REF Term Accession Number assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz soapdenovo2-sequence assembly SOAPdenovo version 2 Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz soapdenovo1-sequence assembly SOAPdenovo version 1 Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size assemblathon-bacteria mock extraction assemblathon-bacteria mock library construction mock sequencing assemblathon-bacteria no ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz ALLPATHS-LG-sequence assembly ALLPATHS-LG Galaxy DT1 T1 http://www.gigasciencejournal.com/content/1/1/18/table/T1 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz soapdenovo2-h-sapiens-sequence assembly SOAPdenovo version 2 Galaxy DT4.Hs.SOAPdenovo2 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 large size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 yes ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz soapdenovo1-h-sapiens-sequence assembly SOAPdenovo version 1 Galaxy DT4.Hs.SOAPdenovo1 T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 large size Homo sapiens reference genome mock extraction Homo sapiens reference genome mock library construction mock sequencing GCA_000001405.1 no ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size YH nucleic acid extraction YH library construction GENOMIC OTHER OTHER PAIRED nucleic acid sequencing Illumina HiSeq 2000 110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2 no ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz ALLPATH-LG-h-sapiens-sequence assembly ALLPATHS-LG Galaxy DT4.Hs.ALLPATH-LG T4 http://www.gigasciencejournal.com/content/1/1/18/table/T4 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG large size # S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz soapdenovo1-s-aureus-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 DT2.Sa.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz soapdenovo2-s-aureus-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 DT2.Sa.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size S.aureus reference genome mock extraction S.aureus reference genome mock library construction mock sequencing NC_010079 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library1 mock library construction mock sequencing Staphylococcus_aureus-Library1 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Staphylococcus_aureus mock extraction Staphylococcus_aureus-Library2 mock library construction mock sequencing Staphylococcus_aureus-Library2 no http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz ALLPATH-LG-s-aureus-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths DT2.Sa.ALLPATH-LG http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz soapdenovo1-r-sphaeroides-sequence assembly SOAPdenovo version 1 Galaxy http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 DT2.Rs.SOAPdenovo1 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz soapdenovo2-r-sphaeroides-sequence assembly SOAPdenovo version 2 Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 DT2.Rs.SOAPdenovo2 http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 small size R.spaeroides reference genome mock extraction R.spaeroides reference genome mock library construction mock sequencing CP000143 no http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library1 mock library construction mock sequencing Rhodobacter_sphaeroides-Library1 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Rhodobacter_sphaeroides mock extraction Rhodobacter_sphaeroides-Library2 mock library construction mock sequencing Rhodobacter_sphaeroides-Library2 no http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz ALLPATH-LG-r-sphaeroides-sequence assembly ALLPATHS-LG Galaxy http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths DT2.Rs.ALLPATH-LG T2 http://www.gigasciencejournal.com/content/1/1/18/table/T2 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG small size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz soapdenovo1-b-impatiens-sequence assembly SOAPdenovo version 1 Galaxy DT3.Bi.SOAPdenovo2 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 2 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz soapdenovo2-b-impatiens-sequence assembly SOAPdenovo version 2 Galaxy DT3.Bi.ALLPATH-LG T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs ALLPATH-LG medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library1 mock library construction mock sequencing Bombus_impatiens_Library1 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library2 mock library construction mock sequencing Bombus_impatiens_Library2 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size Bombus_impatiens mock extraction Bombus_impatiens_Library3 mock library construction mock sequencing Bombus_impatiens_Library3 no http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz ALLPATH-LG-b-impatiens-sequence assembly ALLPATHS-LG Galaxy DT3.Bi.SOAPdenovo1 T3 http://www.gigasciencejournal.com/content/1/1/18/table/T3 nanopublication Nanopub http://w3id.org/isa/soapdenovo2/nanopubs SOAPdenovo version 1 medium size \ No newline at end of file diff --git a/isa-tab/i_Investigation.txt b/isa-tab/i_Investigation.txt index 29ad7f0..ea928f7 100644 --- a/isa-tab/i_Investigation.txt +++ b/isa-tab/i_Investigation.txt @@ -1,99 +1 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name "EFO" "OBI" "NCBITAXON" "PATO" "ERO" -Term Source File "http://data.bioontology.org/ontologies/EFO" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/ERO" -Term Source Version "110" "21" "2" "160" "13" -Term Source Description "Experimental Factor Ontology" "Ontology for Biomedical Investigations" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Phenotypic Quality Ontology" "Eagle-I Research Resource Ontology" -INVESTIGATION -Investigation Identifier "SOAPdenovo2" -Investigation Title "Investigation" -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment [Created with configuration] "" -Comment [Last Opened With Configuration] "" -Comment[Created With Configuration] "" -Comment[Last Opened With Configuration] "" -INVESTIGATION PUBLICATIONS -Investigation PubMed ID "" -Investigation Publication DOI "" -Investigation Publication Author List "" -Investigation Publication Title "" -Investigation Publication Status "" -Investigation Publication Status Term Accession Number "" -Investigation Publication Status Term Source REF "" -INVESTIGATION CONTACTS -Investigation Person Last Name "" -Investigation Person First Name "" -Investigation Person Mid Initials "" -Investigation Person Email "" -Investigation Person Phone "" -Investigation Person Fax "" -Investigation Person Address "" -Investigation Person Affiliation "" -Investigation Person Roles "" -Investigation Person Roles Term Accession Number "" -Investigation Person Roles Term Source REF "" -STUDY -Study Identifier "SOAPdenovo2" -Study Title "SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler" -Study Description "Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption." -Comment[Study Grant Number] "2011CB809203" -Comment[Study Funding Agency] "State Key Development Program for Basic Research of China-973 Program" -Study Submission Date "" -Study Public Release Date "" -Study File Name "s_SOAPdenovo2.txt" -Comment[Experimental Metadata Licence] "http://creativecommons.org/publicdomain/zero/1.0/" -STUDY DESIGN DESCRIPTORS -Study Design Type "software testing objective" "factorial design" -Study Design Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000242" "http://purl.obolibrary.org/obo/OBI_0500014" -Study Design Type Term Source REF "OBI" "OBI" -STUDY PUBLICATIONS -Study PubMed ID "23587118" -Study Publication DOI "10.1186/2047-217X-1-18" -Study Publication Author List "Ruibang Luo et al." -Study Publication Title "SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler" -Study Publication Status "published" -Study Publication Status Term Accession Number "" -Study Publication Status Term Source REF "" -STUDY FACTORS -Study Factor Name "sequence assembly algorithm" "genome size" -Study Factor Type "sequence assembly algorithm" "size" -Study Factor Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0001522" "http://purl.obolibrary.org/obo/PATO_0000117" -Study Factor Type Term Source REF "OBI" "PATO" -STUDY ASSAYS -Study Assay File Name "a_assay_soapdenovo2.txt" -Study Assay Measurement Type "genome sequencing" -Study Assay Measurement Type Term Accession Number "" -Study Assay Measurement Type Term Source REF "" -Study Assay Technology Type "nucleotide sequencing" -Study Assay Technology Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000626" -Study Assay Technology Type Term Source REF "OBI" -Study Assay Technology Platform "" -STUDY PROTOCOLS -Study Protocol Name "sample collection" "soapdenovo2-sequence assembly" "soapdenovo1-sequence assembly" "ALLPATHS-LG-sequence assembly" "soapdenovo1-h-sapiens-sequence assembly" "soapdenovo2-h-sapiens-sequence assembly" "ALLPATH-LG-h-sapiens-sequence assembly" "soapdenovo1-b-impatiens-sequence assembly" "soapdenovo2-b-impatiens-sequence assembly" "ALLPATH-LG-b-impatiens-sequence assembly" "soapdenovo1-s-aureus-sequence assembly" "soapdenovo2-s-aureus-sequence assembly" "ALLPATH-LG-s-aureus-sequence assembly" "soapdenovo1-r-sphaeroides-sequence assembly" "soapdenovo2-r-sphaeroides-sequence assembly" "ALLPATH-LG-r-sphaeroides-sequence assembly" "sequence assembly" "nucleic acid extraction" "library construction" "nucleic acid sequencing" "data download" "mock extraction" "mock library construction" "mock sequencing" "nanopublication" -Study Protocol Type "specimen collection" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "sequence assembly process" "nucleic acid extraction" "library preparation" "nucleic acid sequencing" "information acquisition" "nucleic acid extraction" "library preparation" "nucleic acid sequencing" "data transformation" -Study Protocol Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000659" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0001872" "http://purl.obolibrary.org/obo/OBI_0666667" "http://purl.obolibrary.org/obo/OBI_0000711" "" "http://purl.obolibrary.org/obo/OBI_0600013" "http://purl.obolibrary.org/obo/OBI_0666667" "http://purl.obolibrary.org/obo/OBI_0000711" "" "http://purl.obolibrary.org/obo/OBI_0200000" -Study Protocol Type Term Source REF "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "OBI" "" "OBI" "OBI" "OBI" "" "OBI" -Study Protocol Description "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -Study Protocol URI "" "" "" "" "" "" "" "" "" "" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-3-soapdenovo1-saureus" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-5-allpaths-lg-saureus" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-4-soapdenovo1-rsphaeroides" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-2-soapdenovo2-rsphaeroides" "http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-6-allpaths-lg-rsphaeroides" " http://dx.doi.org/10.5524/100044" "" "" "" "" "" "" "" "" -Study Protocol Version "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -Study Protocol Parameters Name "" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "software location;sequence assembly algorithm;software script;workflow url" "" "library selection;library layout;library strategy;library source" "base caller;quality scorer;sequencing instrument" "" "" "" "" "" -Study Protocol Parameters Name Term Accession Number "" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" "" ";;;" ";;" "" "" "" "" "" -Study Protocol Parameters Name Term Source REF "" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" ";;;" "" ";;;" ";;" "" "" "" "" "" -Study Protocol Components Name "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -Study Protocol Components Type "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" -STUDY CONTACTS -Study Person Last Name "Edmunds" "Luo" "Lam" "Li" "Gonzalez-Beltran" "Rocca-Serra" -Study Person First Name "Scott" "Ruibang" "Tak-Wah" "Peter" "Alejandra" "Philippe" -Study Person Mid Initials "" "" "" "" "" "" -Study Person Email "scott@gigasciencejournal.com" "" " twlam@cs.hku.hk" "peter@gigasciencejournal.com" "alejandra.gonzalezbeltran@oerc.ox.ac.uk" "philippe.rocca-serra@oerc.ox.ac.uk" -Study Person Phone "" "" "" "" "" "" -Study Person Fax "" "" "" "" "" "" -Study Person Address "Shenzhen,China" "Shenzhen, China" "Hong Kong" "Shenzhen,China" "University of Oxford" "University of Oxford" -Study Person Affiliation "Gigascience" "Beigjing Genome Institute" "HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong," "Gigascience" "Oxford e-Research Centre" "Oxford e-Research Centre" -Study Person Roles "journal editor" "data producer" "data producer" "responsible for Galaxy workflows" "software architect responsible for ISA-TAB creation, conversion to RDF and nanopublication" "data manager responsible for ISA-TAB creation, conversion to RDF and nanopublication" -Study Person Roles Term Accession Number "" "" "" "" "" "" -Study Person Roles Term Source REF "" "" "" "" "" "" -Comment[Study Person REF] "http://orcid.org/0000-0001-6444-1436" "http://orcid.org/0000-0001-9711-6533" "http://orcid.org/0000-0003-4676-8587" "http://orcid.org/0000-0001-9602-9550" "http://orcid.org/0000-0003-3499-8262" "http://orcid.org/0000-0001-9853-5668" +ONTOLOGY SOURCE REFERENCE Term Source Name EFO OBI NCBITAXON PATO ERO Term Source File http://data.bioontology.org/ontologies/EFO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/PATO http://data.bioontology.org/ontologies/ERO Term Source Version 110 21 2 160 13 Term Source Description Experimental Factor Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Phenotypic Quality Ontology Eagle-I Research Resource Ontology INVESTIGATION Investigation Identifier SOAPdenovo2 Investigation Title Investigation Investigation Description Investigation Submission Date Investigation Public Release Date Comment [Created with configuration] Comment [Last Opened With Configuration] Comment[Created With Configuration] Comment[Last Opened With Configuration] INVESTIGATION PUBLICATIONS Investigation PubMed ID Investigation Publication DOI Investigation Publication Author List Investigation Publication Title Investigation Publication Status Investigation Publication Status Term Accession Number Investigation Publication Status Term Source REF INVESTIGATION CONTACTS Investigation Person Last Name Investigation Person First Name Investigation Person Mid Initials Investigation Person Email Investigation Person Phone Investigation Person Fax Investigation Person Address Investigation Person Affiliation Investigation Person Roles Investigation Person Roles Term Accession Number Investigation Person Roles Term Source REF STUDY Study Identifier SOAPdenovo2 Study Title SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Study Description "Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption." Comment[Study Grant Number] 2011CB809203 Comment[Study Funding Agency] State Key Development Program for Basic Research of China-973 Program Study Submission Date Study Public Release Date Study File Name s_SOAPdenovo2.txt Comment[Experimental Metadata Licence] http://creativecommons.org/publicdomain/zero/1.0/ STUDY DESIGN DESCRIPTORS Study Design Type software testing objective factorial design Study Design Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000242 http://purl.obolibrary.org/obo/OBI_0500014 Study Design Type Term Source REF OBI OBI STUDY PUBLICATIONS Study PubMed ID 23587118 Study Publication DOI 10.1186/2047-217X-1-18 Study Publication Author List Ruibang Luo et al. Study Publication Title SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Study Publication Status published Study Publication Status Term Accession Number Study Publication Status Term Source REF STUDY FACTORS Study Factor Name sequence assembly algorithm genome size Study Factor Type sequence assembly algorithm size Study Factor Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0001522 http://purl.obolibrary.org/obo/PATO_0000117 Study Factor Type Term Source REF OBI PATO STUDY ASSAYS Study Assay File Name a_assay_soapdenovo2.txt Study Assay Measurement Type genome sequencing Study Assay Measurement Type Term Accession Number Study Assay Measurement Type Term Source REF Study Assay Technology Type nucleotide sequencing Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 Study Assay Technology Type Term Source REF OBI Study Assay Technology Platform STUDY PROTOCOLS Study Protocol Name sample collection soapdenovo2-sequence assembly soapdenovo1-sequence assembly ALLPATHS-LG-sequence assembly soapdenovo1-h-sapiens-sequence assembly soapdenovo2-h-sapiens-sequence assembly ALLPATH-LG-h-sapiens-sequence assembly soapdenovo1-b-impatiens-sequence assembly soapdenovo2-b-impatiens-sequence assembly ALLPATH-LG-b-impatiens-sequence assembly soapdenovo1-s-aureus-sequence assembly soapdenovo2-s-aureus-sequence assembly ALLPATH-LG-s-aureus-sequence assembly soapdenovo1-r-sphaeroides-sequence assembly soapdenovo2-r-sphaeroides-sequence assembly ALLPATH-LG-r-sphaeroides-sequence assembly sequence assembly nucleic acid extraction library construction nucleic acid sequencing data download mock extraction mock library construction mock sequencing nanopublication Study Protocol Type specimen collection sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process nucleic acid extraction library preparation nucleic acid sequencing information acquisition nucleic acid extraction library preparation nucleic acid sequencing data transformation Study Protocol Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000659 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/OBI_0000711 http://purl.obolibrary.org/obo/OBI_0600013 http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/OBI_0000711 http://purl.obolibrary.org/obo/OBI_0200000 Study Protocol Type Term Source REF OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI Study Protocol Description Study Protocol URI http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-allpaths http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-soapdenovo2 http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-allpaths http://dx.doi.org/10.5524/100044 Study Protocol Version Study Protocol Parameters Name software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url library selection;library layout;library strategy;library source base caller;quality scorer;sequencing instrument Study Protocol Parameters Name Term Accession Number ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;; Study Protocol Parameters Name Term Source REF ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;; Study Protocol Components Name Study Protocol Components Type Study Protocol Components Type Term Accession Number Study Protocol Components Type Term Source REF STUDY CONTACTS Study Person Last Name Edmunds Luo Lam Li Gonzalez-Beltran Rocca-Serra Study Person First Name Scott Ruibang Tak-Wah Peter Alejandra Philippe Study Person Mid Initials Study Person Email scott@gigasciencejournal.com twlam@cs.hku.hk peter@gigasciencejournal.com alejandra.gonzalezbeltran@oerc.ox.ac.uk philippe.rocca-serra@oerc.ox.ac.uk Study Person Phone Study Person Fax Study Person Address "Shenzhen,China" "Shenzhen, China" Hong Kong "Shenzhen,China" University of Oxford University of Oxford Study Person Affiliation Gigascience Beigjing Genome Institute "HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong," Gigascience Oxford e-Research Centre Oxford e-Research Centre Study Person Roles journal editor data producer data producer responsible for Galaxy workflows "software architect responsible for ISA-TAB creation, conversion to RDF and nanopublication" "data manager responsible for ISA-TAB creation, conversion to RDF and nanopublication" Study Person Roles Term Accession Number Study Person Roles Term Source REF Comment[Study Person REF] http://orcid.org/0000-0001-6444-1436 http://orcid.org/0000-0001-9711-6533 http://orcid.org/0000-0003-4676-8587 http://orcid.org/0000-0001-9602-9550 http://orcid.org/0000-0003-3499-8262 http://orcid.org/0000-0001-9853-5668 \ No newline at end of file