diff --git a/linkedISA/soapdenovo2.rdf b/linkedISA/soapdenovo2.rdf index f878efc..394d6e4 100644 --- a/linkedISA/soapdenovo2.rdf +++ b/linkedISA/soapdenovo2.rdf @@ -660,457 +660,446 @@ - + - + Scott Edmunds scott@gigasciencejournal.com http://orcid.org/0000-0001-6444-1436 - + - + - + - + Peter Li peter@gigasciencejournal.com http://orcid.org/0000-0001-9602-9550 - + - + - + - + Ruibang Luo http://orcid.org/0000-0001-9711-6533 - + - + - + - + Philippe Rocca-Serra philippe.rocca-serra@oerc.ox.ac.uk http://orcid.org/0000-0001-9853-5668 - + - + - + - + Alejandra Gonzalez-Beltran alejandra.gonzalezbeltran@oerc.ox.ac.uk http://orcid.org/0000-0003-3499-8262 - + - + - + - + Tak-Wah Lam twlam@cs.hku.hk http://orcid.org/0000-0003-4676-8587 - + - + - + - + - + mock extraction OBI:nucleic acid extraction - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/1 - - - - - - - - - - - - soapdenovo2-h-sapiens-sequence assembly - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/10 - - - - - - - - - - - - - - - soapdenovo1-h-sapiens-sequence assembly - OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/11 - - - - - + + - + - - - ALLPATH-LG-h-sapiens-sequence assembly - OBI:sequence assembly process + + + nucleic acid extraction + OBI:nucleic acid extraction http://w3id.org/isa/soapdenovo2/assay_protocol_ref/12 - - - - - + + - + - - - soapdenovo1-s-aureus-sequence assembly - OBI:sequence assembly process + + + mock library construction + OBI:library preparation http://w3id.org/isa/soapdenovo2/assay_protocol_ref/13 - - - - - - + + - + - - - soapdenovo2-s-aureus-sequence assembly - OBI:sequence assembly process + + + library construction + OBI:library preparation http://w3id.org/isa/soapdenovo2/assay_protocol_ref/14 - - - - + + + - + - - - ALLPATH-LG-s-aureus-sequence assembly - OBI:sequence assembly process + + mock sequencing http://w3id.org/isa/soapdenovo2/assay_protocol_ref/15 - - - - - - + nucleic acid sequencing + + + - + - - - soapdenovo1-r-sphaeroides-sequence assembly - OBI:sequence assembly process + + nucleic acid sequencing http://w3id.org/isa/soapdenovo2/assay_protocol_ref/16 - - - - - - + nucleic acid sequencing + + + + - + - - soapdenovo2-r-sphaeroides-sequence assembly + + soapdenovo2-sequence assembly OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/17 - - - - - - + + + + + - + - - ALLPATH-LG-r-sphaeroides-sequence assembly + + soapdenovo1-sequence assembly OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/18 - - - - - - + + + + + - + - - soapdenovo1-b-impatiens-sequence assembly + + ALLPATHS-LG-sequence assembly OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/19 - - - - - - - - - - - - - - - nucleic acid extraction - OBI:nucleic acid extraction - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/2 - - + + + + + - + - - soapdenovo2-b-impatiens-sequence assembly + + soapdenovo2-h-sapiens-sequence assembly OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/20 - - - - - + + + + + - + - - ALLPATH-LG-b-impatiens-sequence assembly + + soapdenovo1-h-sapiens-sequence assembly OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/21 - - - - - + + + + + - + - - - nanopublication - OBI:data transformation + + + ALLPATH-LG-h-sapiens-sequence assembly + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/assay_protocol_ref/22 - - - + + + + + - + - + - - - mock library construction - OBI:library preparation - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/3 - - + + + soapdenovo1-s-aureus-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/23 + + + + + + - + - + - - - library construction - OBI:library preparation - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/4 - - - - - + + + soapdenovo2-s-aureus-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/24 + + + + + + - + - + - - mock sequencing - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/5 - nucleic acid sequencing - - - + + + ALLPATH-LG-s-aureus-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/25 + + + + + + - + - + - - nucleic acid sequencing - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/6 - nucleic acid sequencing - - - - + + + soapdenovo1-r-sphaeroides-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/26 + + + + + + - + - + - - soapdenovo2-sequence assembly + + soapdenovo2-r-sphaeroides-sequence assembly OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/7 - - - - - + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/27 + + + + + + - + - + - - soapdenovo1-sequence assembly + + ALLPATH-LG-r-sphaeroides-sequence assembly OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/8 - - - - - + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/28 + + + + + + - + - + - - ALLPATHS-LG-sequence assembly + + soapdenovo1-b-impatiens-sequence assembly OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/assay_protocol_ref/9 - - - - - + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/29 + + + + + - + - - - Homo sapiens - http://w3id.org/isa/soapdenovo2/characteristics/1 - organism + + + + + soapdenovo2-b-impatiens-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/30 + + + + + + + + + + + + + + + ALLPATH-LG-b-impatiens-sequence assembly + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/31 + + + + + + + + + + + + + + + nanopublication + OBI:data transformation + http://w3id.org/isa/soapdenovo2/assay_protocol_ref/32 + + @@ -1119,9 +1108,9 @@ - NC_010079 - genbank identifier + male http://w3id.org/isa/soapdenovo2/characteristics/10 + phenotypic sex @@ -1130,9 +1119,9 @@ - CP000143 - genbank identifier + Rhodobacter sphaeroides http://w3id.org/isa/soapdenovo2/characteristics/11 + organism @@ -1141,75 +1130,86 @@ - GCA_000001405.1 - genbank identifier + Staphylococcus aureus http://w3id.org/isa/soapdenovo2/characteristics/12 + organism - + - + - Han Chinese - ethnicity - http://w3id.org/isa/soapdenovo2/characteristics/2 + Bombus impatiens + http://w3id.org/isa/soapdenovo2/characteristics/13 + organism - + - + - male - http://w3id.org/isa/soapdenovo2/characteristics/3 - phenotypic sex + Bacteria + http://w3id.org/isa/soapdenovo2/characteristics/14 + organism - + - + - Rhodobacter sphaeroides - http://w3id.org/isa/soapdenovo2/characteristics/4 - organism + USA300_TCH1516 + http://w3id.org/isa/soapdenovo2/characteristics/15 + strain - + - + - Staphylococcus aureus - http://w3id.org/isa/soapdenovo2/characteristics/5 - organism + Caucasian + ethnicity + http://w3id.org/isa/soapdenovo2/characteristics/16 - + - + - Bombus impatiens - http://w3id.org/isa/soapdenovo2/characteristics/6 - organism + NC_010079 + genbank identifier + http://w3id.org/isa/soapdenovo2/characteristics/17 - + - + - Bacteria - http://w3id.org/isa/soapdenovo2/characteristics/7 - organism + CP000143 + genbank identifier + http://w3id.org/isa/soapdenovo2/characteristics/18 + + + + + + + + + GCA_000001405.1 + genbank identifier + http://w3id.org/isa/soapdenovo2/characteristics/19 @@ -1218,9 +1218,9 @@ - USA300_TCH1516 + Homo sapiens http://w3id.org/isa/soapdenovo2/characteristics/8 - strain + organism @@ -1229,68 +1229,137 @@ - Caucasian + Han Chinese ethnicity http://w3id.org/isa/soapdenovo2/characteristics/9 - + + + + + + + DT2.Sa.SOAPdenovo2 + http://w3id.org/isa/soapdenovo2/data_transformation/10 + + + + + + + + + + + + + + + + - + - - - DT1 - http://w3id.org/isa/soapdenovo2/data_transformation/1 - - - - - - - - - - - - + + + DT2.Sa.ALLPATH-LG + http://w3id.org/isa/soapdenovo2/data_transformation/11 + + + + + + + + + + + + - + - + - - + + + DT2.Rs.SOAPdenovo1 + http://w3id.org/isa/soapdenovo2/data_transformation/12 + + + + + + + + + + + + + + + + + + + + + + DT2.Rs.SOAPdenovo2 + http://w3id.org/isa/soapdenovo2/data_transformation/13 + + + + + + + + + + + + + + + + + + + + + DT2.Rs.ALLPATH-LG - http://w3id.org/isa/soapdenovo2/data_transformation/10 - + http://w3id.org/isa/soapdenovo2/data_transformation/14 + - - - - - + + + + + - + - + - - + + DT3.Bi.SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/data_transformation/11 - + http://w3id.org/isa/soapdenovo2/data_transformation/15 + @@ -1300,23 +1369,23 @@ - - - - - + + + + + - + - + - - + + DT3.Bi.ALLPATH-LG - http://w3id.org/isa/soapdenovo2/data_transformation/12 - + http://w3id.org/isa/soapdenovo2/data_transformation/16 + @@ -1326,23 +1395,23 @@ - - - - - + + + + + - + - + - - + + DT3.Bi.SOAPdenovo1 - http://w3id.org/isa/soapdenovo2/data_transformation/13 - + http://w3id.org/isa/soapdenovo2/data_transformation/17 + @@ -1352,23 +1421,23 @@ - - - - - + + + + + - + - + - - + + Nanopub - http://w3id.org/isa/soapdenovo2/data_transformation/14 - + http://w3id.org/isa/soapdenovo2/data_transformation/18 + @@ -1379,56 +1448,46 @@ - - - - - + + + + + - + - + - - - DT4.Hs.SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/data_transformation/2 - - - - - - - - - - - - - - - - - - - - - - + + + DT1 + http://w3id.org/isa/soapdenovo2/data_transformation/5 + + + + + + + + + + + + - + - + - - - DT4.Hs.SOAPdenovo1 - http://w3id.org/isa/soapdenovo2/data_transformation/3 - + + + DT4.Hs.SOAPdenovo2 + http://w3id.org/isa/soapdenovo2/data_transformation/6 + @@ -1445,23 +1504,23 @@ - - - - - + + + + + - + - + - - - DT4.Hs.ALLPATH-LG - http://w3id.org/isa/soapdenovo2/data_transformation/4 - + + + DT4.Hs.SOAPdenovo1 + http://w3id.org/isa/soapdenovo2/data_transformation/7 + @@ -1478,162 +1537,103 @@ - - - - - - - - - - - - - - - DT2.Sa.SOAPdenovo1 - http://w3id.org/isa/soapdenovo2/data_transformation/5 - - - - - - - - - - - - - - - - - - - - - - DT2.Sa.SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/data_transformation/6 - - - - - - - - - - - - - - - - - - - - - - DT2.Sa.ALLPATH-LG - http://w3id.org/isa/soapdenovo2/data_transformation/7 - - - - - - - - - - - - + + + + + - + - - - DT2.Rs.SOAPdenovo1 + + + DT4.Hs.ALLPATH-LG http://w3id.org/isa/soapdenovo2/data_transformation/8 - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - + - - - DT2.Rs.SOAPdenovo2 + + + DT2.Sa.SOAPdenovo1 http://w3id.org/isa/soapdenovo2/data_transformation/9 - - - - - - - - - - - - + + + + + + + + + + + + - + - + T1 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T1 T1 http://w3id.org/isa/soapdenovo2/derived_data_file/1 - - - - - - - - + + + + + + + + - + - + - + http://w3id.org/isa/soapdenovo2/nanopubs http://w3id.org/isa/soapdenovo2/derived_data_file/10 http://w3id.org/isa/soapdenovo2/nanopubs - - + + @@ -1652,27 +1652,27 @@ - + - + - + T4 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T4 T4 http://w3id.org/isa/soapdenovo2/derived_data_file/2 - - - - - - - - + + + + + + + + @@ -1703,23 +1703,23 @@ - + - + - - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ + + http://gigagalaxy.net/datasets/61b51a387c27054a Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/2c85c3f15080065e/ + http://gigagalaxy.net/datasets/61b51a387c27054a http://w3id.org/isa/soapdenovo2/derived_data_file/3 - - - - + + + + @@ -1730,23 +1730,23 @@ - + - + - - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ + + http://gigagalaxy.net/datasets/241d84796a24640a Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/be5093c3ebf7834a/ + http://gigagalaxy.net/datasets/241d84796a24640a http://w3id.org/isa/soapdenovo2/derived_data_file/4 - - - - + + + + @@ -1757,23 +1757,23 @@ - + - + - - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ + + http://gigagalaxy.net/datasets/a32a1d9364c1b029 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/61bff954c161abc1/ + http://gigagalaxy.net/datasets/a32a1d9364c1b029 http://w3id.org/isa/soapdenovo2/derived_data_file/5 - - - - + + + + @@ -1784,23 +1784,23 @@ - + - + - - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ + + http://gigagalaxy.net/datasets/a1b6cce8a2380c73 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/e61166c8e9600bba/ + http://gigagalaxy.net/datasets/a1b6cce8a2380c73 http://w3id.org/isa/soapdenovo2/derived_data_file/6 - - - - + + + + @@ -1811,23 +1811,23 @@ - + - + - - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ + + http://gigagalaxy.net/datasets/32d48e3506ae8cf7 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/d/7ebdaed75d14007e/ + http://gigagalaxy.net/datasets/32d48e3506ae8cf7 http://w3id.org/isa/soapdenovo2/derived_data_file/7 - - - - + + + + @@ -1838,23 +1838,23 @@ - + - + - - T2 + + http://gigagalaxy.net/datasets/eff20c5ba6bf6f87 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T2 - T2 + http://gigagalaxy.net/datasets/eff20c5ba6bf6f87 http://w3id.org/isa/soapdenovo2/derived_data_file/8 - - - - + + + + @@ -1865,27 +1865,27 @@ - + - + - + T3 Comment[Derived Data File information]:http://www.gigasciencejournal.com/content/1/1/18/table/T3 T3 http://w3id.org/isa/soapdenovo2/derived_data_file/9 - - - - - - - - + + + + + + + + @@ -1902,397 +1902,397 @@ - + - + - + - + assemblathon-bacteria Extract Extract - http://w3id.org/isa/soapdenovo2/extract/1 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/163 + + + + + + + + + - + - + - - Bombus_impatiens_Library1 Extract + + Homo sapiens reference genome Extract Extract - http://w3id.org/isa/soapdenovo2/extract/10 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/164 + + + + + + + + + - + - + - - Bombus_impatiens_Library2 Extract + + YH Extract Extract - http://w3id.org/isa/soapdenovo2/extract/11 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/165 + + + + + + + + + - + - + - - Bombus_impatiens_Library3 Extract + + S.aureus reference genome Extract Extract - http://w3id.org/isa/soapdenovo2/extract/12 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/166 + + + + + + + + + - + - + - - Homo sapiens reference genome Extract + + Staphylococcus_aureus-Library1 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/2 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/167 + + + + + + + + + - + - + - - YH Extract + + Staphylococcus_aureus-Library2 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/3 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/168 + + + + + + + + + - + - + - - S.aureus reference genome Extract + + R.spaeroides reference genome Extract Extract - http://w3id.org/isa/soapdenovo2/extract/4 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/169 + + + + + + + + + - + - + - - Staphylococcus_aureus-Library1 Extract + + Rhodobacter_sphaeroides-Library1 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/5 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/170 + + + + + + + + + - + - + - - Staphylococcus_aureus-Library2 Extract + + Rhodobacter_sphaeroides-Library2 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/6 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/171 + + + + + + + + + - + - + - - R.spaeroides reference genome Extract + + Bombus_impatiens_Library1 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/7 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/172 + + + + + + + + + - + - + - - Rhodobacter_sphaeroides-Library1 Extract + + Bombus_impatiens_Library2 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/8 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/173 + + + + + + + + + - + - + - - Rhodobacter_sphaeroides-Library2 Extract + + Bombus_impatiens_Library3 Extract Extract - http://w3id.org/isa/soapdenovo2/extract/9 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/extract/174 + + + + + + + + + - + - + SOAPdenovo version 2 - http://w3id.org/isa/soapdenovo2/factor_value/1 + http://w3id.org/isa/soapdenovo2/factor_value/50 - + - + small size - http://w3id.org/isa/soapdenovo2/factor_value/2 + http://w3id.org/isa/soapdenovo2/factor_value/51 - + - + SOAPdenovo version 1 - http://w3id.org/isa/soapdenovo2/factor_value/3 + http://w3id.org/isa/soapdenovo2/factor_value/52 - + - + ALLPATH-LG - http://w3id.org/isa/soapdenovo2/factor_value/4 + http://w3id.org/isa/soapdenovo2/factor_value/53 - + - + large size - http://w3id.org/isa/soapdenovo2/factor_value/5 + http://w3id.org/isa/soapdenovo2/factor_value/54 - + - + medium size - http://w3id.org/isa/soapdenovo2/factor_value/6 + http://w3id.org/isa/soapdenovo2/factor_value/55 - + - + - + SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/investigation/1 - + http://w3id.org/isa/soapdenovo2/investigation/2 + - + - + SOAPdenovo2 description - http://w3id.org/isa/soapdenovo2/investigation_description/1 - + http://w3id.org/isa/soapdenovo2/investigation_description/2 + - + - + i_investigation.txt investigation file - - - + + + - + - + SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/investigation_identifier/1 - + http://w3id.org/isa/soapdenovo2/investigation_identifier/2 + - + - + SOAPdenovo2 public release date - http://w3id.org/isa/soapdenovo2/investigation_public_release_date/1 + http://w3id.org/isa/soapdenovo2/investigation_public_release_date/2 - + - + SOAPdenovo2 title - Investigation Investigation - http://w3id.org/isa/soapdenovo2/investigation_title/1 - + Investigation + http://w3id.org/isa/soapdenovo2/investigation_title/2 + - + - + SOAPdenovo2 - - + + - + - + SOAPdenovo2 Created with ISA2OWL converter @@ -2303,26 +2303,14 @@ - + - + SOAPdenovo2 - - - - - - - - - - - - - GENOMIC - http://w3id.org/isa/soapdenovo2/parameter_value/1 - + + + @@ -2332,9 +2320,23 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-1-soapdenovo2-saureus + Galaxy http://w3id.org/isa/soapdenovo2/parameter_value/10 - + + + + + + + + + + + + + + + @@ -2344,9 +2346,13 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-5-allpaths-lg-saureus + SOAPdenovo version 1 http://w3id.org/isa/soapdenovo2/parameter_value/11 - + + + + + @@ -2356,9 +2362,13 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-4-soapdenovo1-rsphaeroides + ALLPATHS-LG http://w3id.org/isa/soapdenovo2/parameter_value/12 - + + + + + @@ -2368,9 +2378,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-2-soapdenovo2-rsphaeroides + http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 http://w3id.org/isa/soapdenovo2/parameter_value/13 - + @@ -2380,45 +2390,57 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-6-allpaths-lg-rsphaeroides + http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 http://w3id.org/isa/soapdenovo2/parameter_value/14 - + - + - + - OTHER - http://w3id.org/isa/soapdenovo2/parameter_value/2 - + http://gigagalaxy.net/u/peterli/h/s-aureus-genome-assembly-using-allpaths + http://w3id.org/isa/soapdenovo2/parameter_value/15 + - + - + - PAIRED - http://w3id.org/isa/soapdenovo2/parameter_value/3 - + http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 + http://w3id.org/isa/soapdenovo2/parameter_value/16 + - + - + - Illumina HiSeq 2000 - http://w3id.org/isa/soapdenovo2/parameter_value/4 - + http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-soapdenovo2 + http://w3id.org/isa/soapdenovo2/parameter_value/17 + + + + + + + + + + + http://gigagalaxy.net/u/peterli/h/r-sphaeroides-genome-assembly-using-allpaths + http://w3id.org/isa/soapdenovo2/parameter_value/18 + @@ -2428,13 +2450,9 @@ - SOAPdenovo version 2 + GENOMIC http://w3id.org/isa/soapdenovo2/parameter_value/5 - - - - @@ -2444,23 +2462,9 @@ - Galaxy + OTHER http://w3id.org/isa/soapdenovo2/parameter_value/6 - - - - - - - - - - - - - - @@ -2470,13 +2474,9 @@ - SOAPdenovo version 1 + PAIRED http://w3id.org/isa/soapdenovo2/parameter_value/7 - - - - - + @@ -2486,13 +2486,9 @@ - ALLPATHS-LG + Illumina HiSeq 2000 http://w3id.org/isa/soapdenovo2/parameter_value/8 - - - - - + @@ -2502,2935 +2498,2939 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/h/rluo2012-example-3-soapdenovo1-saureus + SOAPdenovo version 2 http://w3id.org/isa/soapdenovo2/parameter_value/9 - + + + + + - + - + - + 23587118 23587118 - http://w3id.org/isa/soapdenovo2/publication/1 - - - + http://w3id.org/isa/soapdenovo2/publication/4 + + + - + - + ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz http://w3id.org/isa/soapdenovo2/raw_data_file/1 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/10 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/11 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/12 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/13 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/14 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/15 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110115_I270_FC81CBVABXX_L5_HUMiqvDBTDBCAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/16 - - - - - - - - - - - + + + + + + + + + + + - + - + http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 http://w3id.org/isa/soapdenovo2/raw_data_file/17 http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=161508266&extrafeat=0&maxplex=1 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/18 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/19 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz http://w3id.org/isa/soapdenovo2/raw_data_file/2 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/20 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/21 - - - - - - - - - - - + + + + + + + + + + + - + - + http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 http://w3id.org/isa/soapdenovo2/raw_data_file/22 http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=77386383&extrafeat=0&maxplex=1 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_1.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/23 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/frag_2.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/24 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_1.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/25 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/Data.original/shortjump_2.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/26 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_1.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/27 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/frag_2.fastq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/28 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_1_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/29 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/3 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_1_2_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/30 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_1_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/31 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_9_2_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/32 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_1_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/33 - - - - - - - - - - - + + + + + + + + + + + - + - + http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz http://gage.cbcb.umd.edu/data/Bombus_impatiens/Data.original/s_2_2_sequence.txt.gz http://w3id.org/isa/soapdenovo2/raw_data_file/34 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/4 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/5 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/6 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/7 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/8 - - - - - - - - - - - + + + + + + + + + + + - + - + ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz ftp://climb.genomics.cn/pub/10.5524/100001_101000/100038/data/110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1.fq.gz http://w3id.org/isa/soapdenovo2/raw_data_file/9 - - - - - - - - - - - + + + + + + + + + + + - + - + - + YH Sample Sample - http://w3id.org/isa/soapdenovo2/sample/1 - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/179 + + + + + + + + - + - + - + Rhodobacter_sphaeroides Sample Sample - http://w3id.org/isa/soapdenovo2/sample/2 - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/180 + + + + + + + + - + - + - + Staphylococcus_aureus Sample Sample - http://w3id.org/isa/soapdenovo2/sample/3 - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/181 + + + + + + + + - + - + - + Bombus_impatiens Sample Sample - http://w3id.org/isa/soapdenovo2/sample/4 - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/182 + + + + + + + + - + - + - + assemblathon-bacteria Sample Sample - http://w3id.org/isa/soapdenovo2/sample/5 - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/183 + + + + + + + + - + - + - + S.aureus reference genome Sample Sample - http://w3id.org/isa/soapdenovo2/sample/6 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/184 + + + + + + + + + - + - + - + R.spaeroides reference genome Sample Sample - http://w3id.org/isa/soapdenovo2/sample/7 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/185 + + + + + + + + + - + - + - + Homo sapiens reference genome Sample Sample - http://w3id.org/isa/soapdenovo2/sample/8 - - - - - - - - - + http://w3id.org/isa/soapdenovo2/sample/186 + + + + + + + + + - + - + - + YH Source Source - http://w3id.org/isa/soapdenovo2/source/1 - - - - - - - + http://w3id.org/isa/soapdenovo2/source/21 + + + + + + + - + - + - + Rhodobacter_sphaeroides Source Source - http://w3id.org/isa/soapdenovo2/source/2 - - - - - + http://w3id.org/isa/soapdenovo2/source/22 + + + + + - + - + - + Staphylococcus_aureus Source Source - http://w3id.org/isa/soapdenovo2/source/3 - - - - - + http://w3id.org/isa/soapdenovo2/source/23 + + + + + - + - + - + Bombus_impatiens Source Source - http://w3id.org/isa/soapdenovo2/source/4 - - - - - + http://w3id.org/isa/soapdenovo2/source/24 + + + + + - + - + - + assemblathon-bacteria Source Source - http://w3id.org/isa/soapdenovo2/source/5 - - - - - + http://w3id.org/isa/soapdenovo2/source/25 + + + + + - + - + - + NC_010079 Source Source - http://w3id.org/isa/soapdenovo2/source/6 - - - - - - + http://w3id.org/isa/soapdenovo2/source/26 + + + + + + - + - + - + CP000143 Source Source - http://w3id.org/isa/soapdenovo2/source/7 - - - - - + http://w3id.org/isa/soapdenovo2/source/27 + + + + + - + - + - + GCA_000001405.1 Source Source - http://w3id.org/isa/soapdenovo2/source/8 - - - - - - - + http://w3id.org/isa/soapdenovo2/source/28 + + + + + + + - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/1 - + http://w3id.org/isa/soapdenovo2/source_name/628 + - + - + Rhodobacter_sphaeroides - http://w3id.org/isa/soapdenovo2/source_name/10 + http://w3id.org/isa/soapdenovo2/source_name/629 + - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/100 + Staphylococcus_aureus + http://w3id.org/isa/soapdenovo2/source_name/630 + - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/101 + Bombus_impatiens + http://w3id.org/isa/soapdenovo2/source_name/631 + - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/102 + assemblathon-bacteria + http://w3id.org/isa/soapdenovo2/source_name/632 + - + - + - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/103 + NC_010079 + http://w3id.org/isa/soapdenovo2/source_name/633 + + + + + + + + + + CP000143 + http://w3id.org/isa/soapdenovo2/source_name/634 + + + + + + + + + + GCA_000001405.1 + http://w3id.org/isa/soapdenovo2/source_name/635 + + + + + + + + + + YH + http://w3id.org/isa/soapdenovo2/source_name/636 + + + + + + + + + Rhodobacter_sphaeroides + http://w3id.org/isa/soapdenovo2/source_name/637 + + + + + + + + + Staphylococcus_aureus + http://w3id.org/isa/soapdenovo2/source_name/638 + + + + + + + + + Bombus_impatiens + http://w3id.org/isa/soapdenovo2/source_name/639 + + + + + + + + + assemblathon-bacteria + http://w3id.org/isa/soapdenovo2/source_name/640 + + + + + + + + + S.aureus reference genome + http://w3id.org/isa/soapdenovo2/source_name/641 - + - + - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/104 + R.spaeroides reference genome + http://w3id.org/isa/soapdenovo2/source_name/642 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/105 + Homo sapiens reference genome + http://w3id.org/isa/soapdenovo2/source_name/643 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/106 + assemblathon-bacteria + http://w3id.org/isa/soapdenovo2/source_name/644 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/107 + assemblathon-bacteria + http://w3id.org/isa/soapdenovo2/source_name/645 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/108 + assemblathon-bacteria + http://w3id.org/isa/soapdenovo2/source_name/646 - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/109 + Homo sapiens reference genome + http://w3id.org/isa/soapdenovo2/source_name/647 - + - + - Staphylococcus_aureus - http://w3id.org/isa/soapdenovo2/source_name/11 + YH + http://w3id.org/isa/soapdenovo2/source_name/648 - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/110 + YH + http://w3id.org/isa/soapdenovo2/source_name/649 - + - + - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/111 + YH + http://w3id.org/isa/soapdenovo2/source_name/650 - + - + - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/112 + YH + http://w3id.org/isa/soapdenovo2/source_name/651 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/113 + YH + http://w3id.org/isa/soapdenovo2/source_name/652 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/114 + YH + http://w3id.org/isa/soapdenovo2/source_name/653 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/115 + YH + http://w3id.org/isa/soapdenovo2/source_name/654 - + - + - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/116 + YH + http://w3id.org/isa/soapdenovo2/source_name/655 - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/117 + YH + http://w3id.org/isa/soapdenovo2/source_name/656 - + - + - Bombus_impatiens_Library3 - http://w3id.org/isa/soapdenovo2/source_name/118 + YH + http://w3id.org/isa/soapdenovo2/source_name/657 - + - + - Bombus_impatiens - http://w3id.org/isa/soapdenovo2/source_name/12 + YH + http://w3id.org/isa/soapdenovo2/source_name/658 - + - + - assemblathon-bacteria - http://w3id.org/isa/soapdenovo2/source_name/13 + YH + http://w3id.org/isa/soapdenovo2/source_name/659 - + - + - S.aureus reference genome - http://w3id.org/isa/soapdenovo2/source_name/14 + YH + http://w3id.org/isa/soapdenovo2/source_name/660 - + - + - R.spaeroides reference genome - http://w3id.org/isa/soapdenovo2/source_name/15 + YH + http://w3id.org/isa/soapdenovo2/source_name/661 - + - + Homo sapiens reference genome - http://w3id.org/isa/soapdenovo2/source_name/16 + http://w3id.org/isa/soapdenovo2/source_name/662 - + - + - assemblathon-bacteria - http://w3id.org/isa/soapdenovo2/source_name/17 + YH + http://w3id.org/isa/soapdenovo2/source_name/663 - + - + - assemblathon-bacteria - http://w3id.org/isa/soapdenovo2/source_name/18 + YH + http://w3id.org/isa/soapdenovo2/source_name/664 - + - + - assemblathon-bacteria - http://w3id.org/isa/soapdenovo2/source_name/19 + YH + http://w3id.org/isa/soapdenovo2/source_name/665 - + - + - Rhodobacter_sphaeroides - http://w3id.org/isa/soapdenovo2/source_name/2 - + YH + http://w3id.org/isa/soapdenovo2/source_name/666 - + - + - Homo sapiens reference genome - http://w3id.org/isa/soapdenovo2/source_name/20 + YH + http://w3id.org/isa/soapdenovo2/source_name/667 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/21 + http://w3id.org/isa/soapdenovo2/source_name/668 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/22 + http://w3id.org/isa/soapdenovo2/source_name/669 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/23 + http://w3id.org/isa/soapdenovo2/source_name/670 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/24 + http://w3id.org/isa/soapdenovo2/source_name/671 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/25 + http://w3id.org/isa/soapdenovo2/source_name/672 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/26 + http://w3id.org/isa/soapdenovo2/source_name/673 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/27 + http://w3id.org/isa/soapdenovo2/source_name/674 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/28 + http://w3id.org/isa/soapdenovo2/source_name/675 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/29 + http://w3id.org/isa/soapdenovo2/source_name/676 - + - + - Staphylococcus_aureus - http://w3id.org/isa/soapdenovo2/source_name/3 - + Homo sapiens reference genome + http://w3id.org/isa/soapdenovo2/source_name/677 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/30 + http://w3id.org/isa/soapdenovo2/source_name/678 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/31 + http://w3id.org/isa/soapdenovo2/source_name/679 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/32 + http://w3id.org/isa/soapdenovo2/source_name/680 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/33 + http://w3id.org/isa/soapdenovo2/source_name/681 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/34 + http://w3id.org/isa/soapdenovo2/source_name/682 - + - + - Homo sapiens reference genome - http://w3id.org/isa/soapdenovo2/source_name/35 + YH + http://w3id.org/isa/soapdenovo2/source_name/683 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/36 + http://w3id.org/isa/soapdenovo2/source_name/684 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/37 + http://w3id.org/isa/soapdenovo2/source_name/685 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/38 + http://w3id.org/isa/soapdenovo2/source_name/686 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/39 + http://w3id.org/isa/soapdenovo2/source_name/687 - + - + - Bombus_impatiens - http://w3id.org/isa/soapdenovo2/source_name/4 - + YH + http://w3id.org/isa/soapdenovo2/source_name/688 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/40 + http://w3id.org/isa/soapdenovo2/source_name/689 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/41 + http://w3id.org/isa/soapdenovo2/source_name/690 - + - + YH - http://w3id.org/isa/soapdenovo2/source_name/42 + http://w3id.org/isa/soapdenovo2/source_name/691 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/43 + S.aureus reference genome + http://w3id.org/isa/soapdenovo2/source_name/692 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/44 + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/693 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/45 + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/694 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/46 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/695 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/47 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/696 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/48 + S.aureus reference genome + http://w3id.org/isa/soapdenovo2/source_name/697 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/49 + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/698 - + - + - assemblathon-bacteria - http://w3id.org/isa/soapdenovo2/source_name/5 - + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/699 - + - + - Homo sapiens reference genome - http://w3id.org/isa/soapdenovo2/source_name/50 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/700 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/51 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/701 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/52 + S.aureus reference genome + http://w3id.org/isa/soapdenovo2/source_name/702 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/53 + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/703 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/54 + Staphylococcus_aureus-Library1 + http://w3id.org/isa/soapdenovo2/source_name/704 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/55 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/705 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/56 + Staphylococcus_aureus-Library2 + http://w3id.org/isa/soapdenovo2/source_name/706 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/57 + R.spaeroides reference genome + http://w3id.org/isa/soapdenovo2/source_name/707 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/58 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/708 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/59 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/709 - + - + - NC_010079 - http://w3id.org/isa/soapdenovo2/source_name/6 - + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/710 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/60 + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/711 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/61 + R.spaeroides reference genome + http://w3id.org/isa/soapdenovo2/source_name/712 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/62 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/713 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/63 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/714 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/64 + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/715 - + - + - S.aureus reference genome - http://w3id.org/isa/soapdenovo2/source_name/65 + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/716 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/66 + R.spaeroides reference genome + http://w3id.org/isa/soapdenovo2/source_name/717 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/67 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/718 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/68 + Rhodobacter_sphaeroides-Library1 + http://w3id.org/isa/soapdenovo2/source_name/719 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/69 + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/720 - + - + - CP000143 - http://w3id.org/isa/soapdenovo2/source_name/7 - + Rhodobacter_sphaeroides-Library2 + http://w3id.org/isa/soapdenovo2/source_name/721 - + - + - S.aureus reference genome - http://w3id.org/isa/soapdenovo2/source_name/70 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/722 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/71 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/723 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/72 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/724 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/73 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/725 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/74 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/726 - + - + - S.aureus reference genome - http://w3id.org/isa/soapdenovo2/source_name/75 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/727 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/76 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/728 - + - + - Staphylococcus_aureus-Library1 - http://w3id.org/isa/soapdenovo2/source_name/77 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/729 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/78 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/730 - + - + - Staphylococcus_aureus-Library2 - http://w3id.org/isa/soapdenovo2/source_name/79 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/731 - + - + - GCA_000001405.1 - http://w3id.org/isa/soapdenovo2/source_name/8 - + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/732 - + - + - R.spaeroides reference genome - http://w3id.org/isa/soapdenovo2/source_name/80 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/733 - + - + - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/81 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/734 - + - + - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/82 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/735 - + - + - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/83 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/736 - + - + - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/84 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/737 - + - + - R.spaeroides reference genome - http://w3id.org/isa/soapdenovo2/source_name/85 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/738 - + - + - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/86 + Bombus_impatiens_Library1 + http://w3id.org/isa/soapdenovo2/source_name/739 - + - + - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/87 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/740 - + - + - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/88 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/741 - + - + - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/89 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/742 - + - + - YH - http://w3id.org/isa/soapdenovo2/source_name/9 + Bombus_impatiens_Library2 + http://w3id.org/isa/soapdenovo2/source_name/743 - + - + - R.spaeroides reference genome - http://w3id.org/isa/soapdenovo2/source_name/90 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/744 - + - + - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/91 + Bombus_impatiens_Library3 + http://w3id.org/isa/soapdenovo2/source_name/745 - + - - - Rhodobacter_sphaeroides-Library1 - http://w3id.org/isa/soapdenovo2/source_name/92 + + + + + SOAPdenovo2 + Experimental Metadata Licence: http://creativecommons.org/publicdomain/zero/1.0/ + Study Funding Agency: State Key Development Program for Basic Research of China-973 Program + Study Grant Number: 2011CB809203 + http://w3id.org/isa/soapdenovo2/study/3 + - + - - - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/93 + + + + + assemblathon-bacteria + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/177 + + + + + + + + + - + - - - Rhodobacter_sphaeroides-Library2 - http://w3id.org/isa/soapdenovo2/source_name/94 + + + + + GCA_000001405.1 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/178 + + + + + + + + + - + - - - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/95 + + + + + 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 + Comment[Export]:no + Comment[Export]:yes + http://w3id.org/isa/soapdenovo2/study_assay/179 + + + + + + + + + - + - - - Bombus_impatiens_Library1 - http://w3id.org/isa/soapdenovo2/source_name/96 + + + + + 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/180 + + + + + + + + + - + - - - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/97 + + + + + 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/181 + + + + + + + + + - + - - - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/98 + + + + + 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/182 + + + + + + + + + - + - - - Bombus_impatiens_Library2 - http://w3id.org/isa/soapdenovo2/source_name/99 + + + + + 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/183 + + + + + + + + + - + - - - - - SOAPdenovo2 - Experimental Metadata Licence: http://creativecommons.org/publicdomain/zero/1.0/ - Study Funding Agency: State Key Development Program for Basic Research of China-973 Program - Study Grant Number: 2011CB809203 - http://w3id.org/isa/soapdenovo2/study/1 - - + + + + + 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 + Comment[Export]:no + http://w3id.org/isa/soapdenovo2/study_assay/184 + + + + + + + + + + - + - + - - - assemblathon-bacteria + + + 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/1 - - - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_assay/185 + + + + + + + + + + - + - + - - + + 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_2 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/10 - - - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_assay/186 + + + + + + + + + + - + - + - - + + 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_1 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/11 - - - + http://w3id.org/isa/soapdenovo2/study_assay/187 + + + - - - - - - + + + + + + - + - + - - + + 110114_I481_FC81C7HABXX_L8_HUMiqvDBTDBABPE_2 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/12 - - - + http://w3id.org/isa/soapdenovo2/study_assay/188 + + + - - - - - - + + + + + + - + - + - - + + 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_1 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/13 - - - + http://w3id.org/isa/soapdenovo2/study_assay/189 + + + - - - - - - + + + + + + - + - + - - + + 110115_I125_FC81C7KABXX_L3_HUMiqvDBTDLAAPE_2 Comment[Export]:no - 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http://w3id.org/isa/soapdenovo2/study_assay/19 - - - + http://w3id.org/isa/soapdenovo2/study_assay/195 + + + - - - - - - - - - - - - - - - - GCA_000001405.1 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/2 - - - - - - - - - - + + + + + + - + - + - - + + CP000143 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/20 - - - + http://w3id.org/isa/soapdenovo2/study_assay/196 + + + - - - - - - + + + + + + - + - + - - + + Rhodobacter_sphaeroides-Library1 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/21 - - - + http://w3id.org/isa/soapdenovo2/study_assay/197 + + + - - - - - - + + + + + + - + - + - - + + Rhodobacter_sphaeroides-Library2 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/22 - - - + http://w3id.org/isa/soapdenovo2/study_assay/198 + + + - - - - - - + + + + + + - + - + - - + + Bombus_impatiens_Library1 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/23 - - - + http://w3id.org/isa/soapdenovo2/study_assay/199 + + + - - - - - - + + + + + + - + - + - - + + Bombus_impatiens_Library2 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/24 - - - + http://w3id.org/isa/soapdenovo2/study_assay/200 + + + - - - - - - + + + + + + - + - + - - + + Bombus_impatiens_Library3 Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/25 - - - + http://w3id.org/isa/soapdenovo2/study_assay/201 + + + - - - - - - - - - - - - - - - - 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_1 - Comment[Export]:no - Comment[Export]:yes - http://w3id.org/isa/soapdenovo2/study_assay/3 - - - - - - - - - - - - - - - - - - - - 110112_I199_FC819BBABXX_L3_HUMiqvDBTDWAAPE_2 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/4 - - - - - - - - - - - - - - - - - - - - 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_1 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/5 - - - - - - - - - - - - - - - - - - - - 110114_I481_FC81C7HABXX_L5_HUMiqvDBTDIAAPE_2 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/6 - - - - - - - - - - - - - - - - - - - - 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_1 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/7 - - - - - - - - - - - - - - - - - - - - 110114_I481_FC81C7HABXX_L6_HUMiqvDBTDIBAPE_2 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/8 - - - - - - - - - - - - - - - - - - - - 110114_I481_FC81C7HABXX_L7_HUMiqvDBTDBAAPE_1 - Comment[Export]:no - http://w3id.org/isa/soapdenovo2/study_assay/9 - - - - - - - - - - + + + + + + - + - + a_assay_soapdenovo2.txt - http://w3id.org/isa/soapdenovo2/study_assay_file/1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_assay_file/5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a_assay_soapdenovo2.txt filename - http://w3id.org/isa/soapdenovo2/study_assay_file_name/1 - + http://w3id.org/isa/soapdenovo2/study_assay_file_name/5 + - + - + genome sequencing - http://w3id.org/isa/soapdenovo2/study_assay_measurement_type/1 + http://w3id.org/isa/soapdenovo2/study_assay_measurement_type/4 - + - + OBI:nucleotide sequencing - http://w3id.org/isa/soapdenovo2/study_assay_technology_type/1 + http://w3id.org/isa/soapdenovo2/study_assay_technology_type/3 - + - + SOAPdenovo2 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. 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. - http://w3id.org/isa/soapdenovo2/study_description/1 - - + http://w3id.org/isa/soapdenovo2/study_description/3 + + - + - + SOAPdenovo2 study design execution - http://w3id.org/isa/soapdenovo2/study_design_execution/1 - - + http://w3id.org/isa/soapdenovo2/study_design_execution/3 + + - + - + @@ -5438,276 +5438,276 @@ SOAPdenovo2 study design OBI:factorial design OBI:software testing objective - http://w3id.org/isa/soapdenovo2/study_design_type/1 - - - - - - - - - - - - - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_design_type/3 + + + + + + + + + + + + - - - - - - - - + + + + + + + + + + + + + + + + - + - + - + sequence assembly algorithm - http://w3id.org/isa/soapdenovo2/study_factor/1 - - - - + http://w3id.org/isa/soapdenovo2/study_factor/6 + + + + - + - + - + genome size - http://w3id.org/isa/soapdenovo2/study_factor/2 - - - - + http://w3id.org/isa/soapdenovo2/study_factor/7 + + + + - + - + sequence assembly algorithm - http://w3id.org/isa/soapdenovo2/study_factor_name/1 + http://w3id.org/isa/soapdenovo2/study_factor_name/6 - + - + genome size - http://w3id.org/isa/soapdenovo2/study_factor_name/2 + http://w3id.org/isa/soapdenovo2/study_factor_name/7 - + - + - + s_SOAPdenovo2.txt - http://w3id.org/isa/soapdenovo2/study_file/1 - - - - + http://w3id.org/isa/soapdenovo2/study_file/3 + + + + - + - + s_SOAPdenovo2.txt - http://w3id.org/isa/soapdenovo2/study_file_name/1 - + http://w3id.org/isa/soapdenovo2/study_file_name/3 + - + - + - + ALLPATH-LG| large size - http://w3id.org/isa/soapdenovo2/study_group/1 - - - - - + http://w3id.org/isa/soapdenovo2/study_group/26 + + + + + - + - + - + SOAPdenovo version 1| large size - http://w3id.org/isa/soapdenovo2/study_group/2 - - - - - + http://w3id.org/isa/soapdenovo2/study_group/27 + + + + + - + - + - + ALLPATH-LG| small size - http://w3id.org/isa/soapdenovo2/study_group/3 - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_group/28 + + + + + + + + - + - + - + SOAPdenovo version 1| small size - http://w3id.org/isa/soapdenovo2/study_group/4 - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_group/29 + + + + + + + + - + - + - + SOAPdenovo version 2| large size - http://w3id.org/isa/soapdenovo2/study_group/5 - - - - - + http://w3id.org/isa/soapdenovo2/study_group/30 + + + + + - + - + - + ALLPATH-LG| medium size - http://w3id.org/isa/soapdenovo2/study_group/6 - - - - + http://w3id.org/isa/soapdenovo2/study_group/31 + + + + - + - + - + SOAPdenovo version 2| small size - http://w3id.org/isa/soapdenovo2/study_group/7 - - - - - - - - + http://w3id.org/isa/soapdenovo2/study_group/32 + + + + + + + + - + - + - + SOAPdenovo version 1| medium size - http://w3id.org/isa/soapdenovo2/study_group/8 - - - - + http://w3id.org/isa/soapdenovo2/study_group/33 + + + + - + - + - + SOAPdenovo version 2| medium size - http://w3id.org/isa/soapdenovo2/study_group/9 - - - - + http://w3id.org/isa/soapdenovo2/study_group/34 + + + + - + - + SOAPdenovo2 - http://w3id.org/isa/soapdenovo2/study_identifier/1 - + http://w3id.org/isa/soapdenovo2/study_identifier/3 + @@ -6083,390 +6083,302 @@ - + - + - + sample collection protocol OBI:specimen collection - http://w3id.org/isa/soapdenovo2/study_protocol/1 - - - - - - - - - - ALLPATH-LG-b-impatiens-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/10 - - - - - - - - - - soapdenovo1-s-aureus-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/11 - - - - - - - - - - soapdenovo2-s-aureus-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/12 - - - - - - - - - - ALLPATH-LG-s-aureus-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/13 - - - - - - - - - - soapdenovo1-r-sphaeroides-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/14 - - - - - - - - - - soapdenovo2-r-sphaeroides-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/15 - - - - - - - - - - ALLPATH-LG-r-sphaeroides-sequence assembly protocol - OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/16 - - - - - - - - - - sequence assembly protocol - OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/17 - + - + - - nucleic acid extraction protocol - OBI:nucleic acid extraction + + soapdenovo2-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/18 - + - - - - library construction protocol - OBI:library preparation - http://w3id.org/isa/soapdenovo2/study_protocol/19 - - - - - - - + - - soapdenovo2-sequence assembly protocol + + soapdenovo1-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/2 - + http://w3id.org/isa/soapdenovo2/study_protocol/19 + - + - - nucleic acid sequencing protocol + + ALLPATHS-LG-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/20 - nucleic acid sequencing - + - + - - data download protocol - OBI:information acquisition + + soapdenovo1-h-sapiens-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/21 - + - + - - mock extraction protocol - OBI:nucleic acid extraction + + soapdenovo2-h-sapiens-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/22 - + - + - - mock library construction protocol - OBI:library preparation + + ALLPATH-LG-h-sapiens-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/23 - + - + - - mock sequencing protocol + + soapdenovo1-b-impatiens-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/24 - nucleic acid sequencing - + - + - - nanopublication protocol - OBI:data transformation + + soapdenovo2-b-impatiens-sequence assembly protocol + OBI:sequence assembly process http://w3id.org/isa/soapdenovo2/study_protocol/25 - + - + - + - - soapdenovo1-sequence assembly protocol + + ALLPATH-LG-b-impatiens-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/3 - + http://w3id.org/isa/soapdenovo2/study_protocol/26 + - + - + - - ALLPATHS-LG-sequence assembly protocol + + soapdenovo1-s-aureus-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/4 - + http://w3id.org/isa/soapdenovo2/study_protocol/27 + - + - + - - soapdenovo1-h-sapiens-sequence assembly protocol + + soapdenovo2-s-aureus-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/5 - + http://w3id.org/isa/soapdenovo2/study_protocol/28 + - + - + - - soapdenovo2-h-sapiens-sequence assembly protocol + + ALLPATH-LG-s-aureus-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/6 - + http://w3id.org/isa/soapdenovo2/study_protocol/29 + - + - + - - ALLPATH-LG-h-sapiens-sequence assembly protocol + + soapdenovo1-r-sphaeroides-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/7 - + http://w3id.org/isa/soapdenovo2/study_protocol/30 + - + - + - - soapdenovo1-b-impatiens-sequence assembly protocol + + soapdenovo2-r-sphaeroides-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/8 - + http://w3id.org/isa/soapdenovo2/study_protocol/31 + - + - + - - soapdenovo2-b-impatiens-sequence assembly protocol + + ALLPATH-LG-r-sphaeroides-sequence assembly protocol OBI:sequence assembly process - http://w3id.org/isa/soapdenovo2/study_protocol/9 - + http://w3id.org/isa/soapdenovo2/study_protocol/32 + - + - - - sample collection protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/1 - + + + + sequence assembly protocol + OBI:sequence assembly process + http://w3id.org/isa/soapdenovo2/study_protocol/33 - + - - - ALLPATH-LG-b-impatiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/10 - + + + + nucleic acid extraction protocol + OBI:nucleic acid extraction + http://w3id.org/isa/soapdenovo2/study_protocol/34 - + - - - soapdenovo1-s-aureus-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/11 - + + + + library construction protocol + OBI:library preparation + http://w3id.org/isa/soapdenovo2/study_protocol/35 - + - - - soapdenovo2-s-aureus-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/12 - + + + + nucleic acid sequencing protocol + http://w3id.org/isa/soapdenovo2/study_protocol/36 + nucleic acid sequencing - + - - - ALLPATH-LG-s-aureus-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/13 - + + + + data download protocol + OBI:information acquisition + http://w3id.org/isa/soapdenovo2/study_protocol/37 - + - - - soapdenovo1-r-sphaeroides-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/14 - + + + + mock extraction protocol + OBI:nucleic acid extraction + http://w3id.org/isa/soapdenovo2/study_protocol/38 - + - - - soapdenovo2-r-sphaeroides-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/15 - + + + + mock library construction protocol + OBI:library preparation + http://w3id.org/isa/soapdenovo2/study_protocol/39 - + - - - ALLPATH-LG-r-sphaeroides-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/16 - + + + + mock sequencing protocol + http://w3id.org/isa/soapdenovo2/study_protocol/40 + nucleic acid sequencing + + + + + + + + + + nanopublication protocol + OBI:data transformation + http://w3id.org/isa/soapdenovo2/study_protocol/41 @@ -6475,7 +6387,7 @@ - sequence assembly protocol name + sample collection protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/17 @@ -6486,7 +6398,7 @@ - nucleic acid extraction protocol name + soapdenovo2-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/18 @@ -6497,29 +6409,18 @@ - library construction protocol name + soapdenovo1-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/19 - - - - - soapdenovo2-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/2 - - - - - - nucleic acid sequencing protocol name + ALLPATHS-LG-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/20 @@ -6530,7 +6431,7 @@ - data download protocol name + soapdenovo1-h-sapiens-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/21 @@ -6541,7 +6442,7 @@ - mock extraction protocol name + soapdenovo2-h-sapiens-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/22 @@ -6552,7 +6453,7 @@ - mock library construction protocol name + ALLPATH-LG-h-sapiens-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/23 @@ -6563,7 +6464,7 @@ - mock sequencing protocol name + soapdenovo1-b-impatiens-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/24 @@ -6574,97 +6475,185 @@ - nanopublication protocol name + soapdenovo2-b-impatiens-sequence assembly protocol name http://w3id.org/isa/soapdenovo2/study_protocol_name/25 - + - + - soapdenovo1-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/3 - + ALLPATH-LG-b-impatiens-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/26 + - + - + - ALLPATHS-LG-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/4 - + soapdenovo1-s-aureus-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/27 + - + - + - soapdenovo1-h-sapiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/5 - + soapdenovo2-s-aureus-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/28 + - + - + - soapdenovo2-h-sapiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/6 - + ALLPATH-LG-s-aureus-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/29 + - + - + - ALLPATH-LG-h-sapiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/7 - + soapdenovo1-r-sphaeroides-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/30 + - + - + - soapdenovo1-b-impatiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/8 - + soapdenovo2-r-sphaeroides-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/31 + - + - + - soapdenovo2-b-impatiens-sequence assembly protocol name - http://w3id.org/isa/soapdenovo2/study_protocol_name/9 - + ALLPATH-LG-r-sphaeroides-sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/32 + - + - - - - software location - http://w3id.org/isa/soapdenovo2/study_protocol_parameter/1 + + + sequence assembly protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/33 + + + + + + + + + + nucleic acid extraction protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/34 + + + + + + + + + + library construction protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/35 + + + + + + + + + + nucleic acid sequencing protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/36 + + + + + + + + + + data download protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/37 + + + + + + + + + + mock extraction protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/38 + + + + + + + + + + mock library construction protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/39 + + + + + + + + + + mock sequencing protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/40 + + + + + + + + + + nanopublication protocol name + http://w3id.org/isa/soapdenovo2/study_protocol_name/41 + @@ -6674,7 +6663,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/10 @@ -6685,7 +6674,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/11 @@ -6696,9 +6685,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/12 - @@ -6708,8 +6696,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/13 + @@ -6719,7 +6708,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/14 @@ -6730,7 +6719,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/15 @@ -6741,9 +6730,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/16 - @@ -6753,8 +6741,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/17 + @@ -6764,7 +6753,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/18 @@ -6775,7 +6764,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/19 @@ -6786,7 +6775,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/2 @@ -6797,9 +6786,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/20 - @@ -6809,8 +6797,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/21 + @@ -6820,7 +6809,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/22 @@ -6831,7 +6820,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/23 @@ -6842,9 +6831,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/24 - @@ -6854,8 +6842,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/25 + @@ -6865,7 +6854,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/26 @@ -6876,7 +6865,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/27 @@ -6887,9 +6876,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/28 - @@ -6899,8 +6887,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/29 + @@ -6910,7 +6899,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/3 @@ -6921,7 +6910,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/30 @@ -6932,7 +6921,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/31 @@ -6943,9 +6932,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/32 - @@ -6955,8 +6943,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/33 + @@ -6966,7 +6955,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/34 @@ -6977,7 +6966,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/35 @@ -6988,9 +6977,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/36 - @@ -7000,8 +6988,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/37 + @@ -7011,7 +7000,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/38 @@ -7022,7 +7011,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/39 @@ -7033,9 +7022,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/4 - @@ -7045,9 +7033,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/40 - @@ -7057,8 +7044,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/41 + @@ -7068,7 +7056,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/42 @@ -7079,7 +7067,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/43 @@ -7090,9 +7078,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/44 - @@ -7102,8 +7089,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/45 + @@ -7113,7 +7101,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/46 @@ -7124,7 +7112,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/47 @@ -7135,9 +7123,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/48 - @@ -7147,8 +7134,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/49 + @@ -7158,8 +7146,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/5 + @@ -7169,7 +7158,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/50 @@ -7180,7 +7169,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/51 @@ -7191,9 +7180,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/52 - @@ -7203,8 +7191,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/53 + @@ -7214,7 +7203,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/54 @@ -7225,7 +7214,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/55 @@ -7236,9 +7225,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/56 - @@ -7248,8 +7236,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/57 + @@ -7259,7 +7248,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/58 @@ -7270,7 +7259,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/59 @@ -7281,7 +7270,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/6 @@ -7292,9 +7281,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/60 - @@ -7304,8 +7292,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/61 + @@ -7315,7 +7304,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameter/62 @@ -7326,7 +7315,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/63 @@ -7337,9 +7326,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/64 - @@ -7349,8 +7337,9 @@ - library selection + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/65 + @@ -7360,7 +7349,7 @@ - library layout + library selection http://w3id.org/isa/soapdenovo2/study_protocol_parameter/66 @@ -7371,7 +7360,7 @@ - library strategy + library layout http://w3id.org/isa/soapdenovo2/study_protocol_parameter/67 @@ -7382,9 +7371,8 @@ - library source + library strategy http://w3id.org/isa/soapdenovo2/study_protocol_parameter/68 - @@ -7394,8 +7382,9 @@ - base caller + library source http://w3id.org/isa/soapdenovo2/study_protocol_parameter/69 + @@ -7405,7 +7394,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameter/7 @@ -7416,7 +7405,7 @@ - quality scorer + base caller http://w3id.org/isa/soapdenovo2/study_protocol_parameter/70 @@ -7427,9 +7416,20 @@ - sequencing instrument + quality scorer http://w3id.org/isa/soapdenovo2/study_protocol_parameter/71 - + + + + + + + + + + sequencing instrument + http://w3id.org/isa/soapdenovo2/study_protocol_parameter/72 + @@ -7439,9 +7439,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameter/8 - @@ -7451,18 +7450,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameter/9 - - - - - - - - - software location - http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/1 + @@ -7471,7 +7461,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/10 @@ -7481,7 +7471,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/11 @@ -7491,9 +7481,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/12 - @@ -7502,8 +7491,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/13 + @@ -7512,7 +7502,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/14 @@ -7522,7 +7512,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/15 @@ -7532,9 +7522,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/16 - @@ -7543,8 +7532,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/17 + @@ -7553,7 +7543,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/18 @@ -7563,7 +7553,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/19 @@ -7573,7 +7563,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/2 @@ -7583,9 +7573,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/20 - @@ -7594,8 +7583,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/21 + @@ -7604,7 +7594,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/22 @@ -7614,7 +7604,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/23 @@ -7624,9 +7614,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/24 - @@ -7635,8 +7624,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/25 + @@ -7645,7 +7635,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/26 @@ -7655,7 +7645,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/27 @@ -7665,9 +7655,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/28 - @@ -7676,8 +7665,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/29 + @@ -7686,7 +7676,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/3 @@ -7696,7 +7686,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/30 @@ -7706,7 +7696,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/31 @@ -7716,9 +7706,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/32 - @@ -7727,8 +7716,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/33 + @@ -7737,7 +7727,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/34 @@ -7747,7 +7737,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/35 @@ -7757,9 +7747,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/36 - @@ -7768,8 +7757,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/37 + @@ -7778,7 +7768,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/38 @@ -7788,7 +7778,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/39 @@ -7798,9 +7788,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/4 - @@ -7809,9 +7798,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/40 - @@ -7820,8 +7808,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/41 + @@ -7830,7 +7819,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/42 @@ -7840,7 +7829,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/43 @@ -7850,9 +7839,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/44 - @@ -7861,8 +7849,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/45 + @@ -7871,7 +7860,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/46 @@ -7881,7 +7870,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/47 @@ -7891,9 +7880,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/48 - @@ -7902,8 +7890,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/49 + @@ -7912,8 +7901,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/5 + @@ -7922,7 +7912,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/50 @@ -7932,7 +7922,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/51 @@ -7942,9 +7932,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/52 - @@ -7953,8 +7942,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/53 + @@ -7963,7 +7953,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/54 @@ -7973,7 +7963,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/55 @@ -7983,9 +7973,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/56 - @@ -7994,8 +7983,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/57 + @@ -8004,7 +7994,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/58 @@ -8014,7 +8004,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/59 @@ -8024,7 +8014,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/6 @@ -8034,9 +8024,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/60 - @@ -8045,8 +8034,9 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/61 + @@ -8055,7 +8045,7 @@ - sequence assembly algorithm + software location http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/62 @@ -8065,7 +8055,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/63 @@ -8075,9 +8065,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/64 - @@ -8086,8 +8075,9 @@ - library selection + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/65 + @@ -8096,7 +8086,7 @@ - library layout + library selection http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/66 @@ -8106,7 +8096,7 @@ - library strategy + library layout http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/67 @@ -8116,9 +8106,8 @@ - library source + library strategy http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/68 - @@ -8127,8 +8116,9 @@ - base caller + library source http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/69 + @@ -8137,7 +8127,7 @@ - software script + sequence assembly algorithm http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/7 @@ -8147,7 +8137,7 @@ - quality scorer + base caller http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/70 @@ -8157,9 +8147,19 @@ - sequencing instrument + quality scorer http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/71 - + + + + + + + + + sequencing instrument + http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/72 + @@ -8168,9 +8168,8 @@ - workflow url + software script http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/8 - @@ -8179,37 +8178,38 @@ - software location + workflow url http://w3id.org/isa/soapdenovo2/study_protocol_parameters_name/9 + - + - + - + sample collection OBI:specimen collection - http://w3id.org/isa/soapdenovo2/study_protocol_ref/1 - - + http://w3id.org/isa/soapdenovo2/study_protocol_ref/2 + + - + - + - + data download OBI:information acquisition - http://w3id.org/isa/soapdenovo2/study_protocol_ref/2 - - + http://w3id.org/isa/soapdenovo2/study_protocol_ref/3 + + @@ -8217,9 +8217,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-3-soapdenovo1-saureus + http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 http://w3id.org/isa/soapdenovo2/study_protocol_uri/1 - + @@ -8228,9 +8228,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus + http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 http://w3id.org/isa/soapdenovo2/study_protocol_uri/2 - + @@ -8239,9 +8239,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-5-allpaths-lg-saureus + http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-allpaths http://w3id.org/isa/soapdenovo2/study_protocol_uri/3 - + @@ -8250,9 +8250,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-4-soapdenovo1-rsphaeroides + http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 http://w3id.org/isa/soapdenovo2/study_protocol_uri/4 - + @@ -8261,9 +8261,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-2-soapdenovo2-rsphaeroides + http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-soapdenovo2 http://w3id.org/isa/soapdenovo2/study_protocol_uri/5 - + @@ -8272,9 +8272,9 @@ - http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-6-allpaths-lg-rsphaeroides + http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-allpaths http://w3id.org/isa/soapdenovo2/study_protocol_uri/6 - + @@ -8285,7 +8285,7 @@ http://dx.doi.org/10.5524/100044 http://w3id.org/isa/soapdenovo2/study_protocol_uri/7 - + @@ -8296,7 +8296,7 @@ Ruibang Luo et al. http://w3id.org/isa/soapdenovo2/study_publication_author_list/1 - + @@ -8307,7 +8307,7 @@ 10.1186/2047-217X-1-18 http://w3id.org/isa/soapdenovo2/study_publication_doi/1 - + @@ -8318,7 +8318,7 @@ SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler http://w3id.org/isa/soapdenovo2/study_publication_title/1 - + @@ -8329,22 +8329,22 @@ 23587118 http://w3id.org/isa/soapdenovo2/study_pubmed_id/1 - + - + - + SOAPdenovo2 title - SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler - http://w3id.org/isa/soapdenovo2/study_title/1 - - + SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler + http://w3id.org/isa/soapdenovo2/study_title/3 + + diff --git a/ro/Galaxy-wfdesc.rdf b/ro/Galaxy-wfdesc.rdf index a0a7329..09cb9f9 100644 --- a/ro/Galaxy-wfdesc.rdf +++ b/ro/Galaxy-wfdesc.rdf @@ -59,7 +59,7 @@ - + Galaxy workflow for reproducing Table 2 of SOAPdenovo paper Galaxy workflow for reproducing Table 2 of SOAPdenovo paper @@ -68,7 +68,7 @@ Galaxy workflow for reproducing Table 2 of SOAPdenovo paper - + diff --git a/ro/make.sh b/ro/make.sh index f23d2d6..1d25ba8 100755 --- a/ro/make.sh +++ b/ro/make.sh @@ -78,7 +78,7 @@ ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/21 # Add workflow description (wfdesc) -# http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus +# http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 ro annotate Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga -g Galaxy-wfdesc.rdf