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i_Investigation.txt
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ONTOLOGY SOURCE REFERENCE Term Source Name EFO OBI NCBITAXON PATO ERO Term Source File http://data.bioontology.org/ontologies/EFO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/PATO http://data.bioontology.org/ontologies/ERO Term Source Version 110 21 2 160 13 Term Source Description Experimental Factor Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Phenotypic Quality Ontology Eagle-I Research Resource Ontology INVESTIGATION Investigation Identifier SOAPdenovo2 Investigation Title Investigation Investigation Description Investigation Submission Date Investigation Public Release Date Comment [Created with configuration] Comment [Last Opened With Configuration] Comment[Created With Configuration] Comment[Last Opened With Configuration] INVESTIGATION PUBLICATIONS Investigation PubMed ID Investigation Publication DOI Investigation Publication Author List Investigation Publication Title Investigation Publication Status Investigation Publication Status Term Accession Number Investigation Publication Status Term Source REF INVESTIGATION CONTACTS Investigation Person Last Name Investigation Person First Name Investigation Person Mid Initials Investigation Person Email Investigation Person Phone Investigation Person Fax Investigation Person Address Investigation Person Affiliation Investigation Person Roles Investigation Person Roles Term Accession Number Investigation Person Roles Term Source REF STUDY Study Identifier SOAPdenovo2 Study Title SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Study Description "Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption." Comment[Study Grant Number] 2011CB809203 Comment[Study Funding Agency] State Key Development Program for Basic Research of China-973 Program Study Submission Date Study Public Release Date Study File Name s_SOAPdenovo2.txt Comment[Experimental Metadata Licence] http://creativecommons.org/publicdomain/zero/1.0/ STUDY DESIGN DESCRIPTORS Study Design Type software testing objective factorial design Study Design Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000242 http://purl.obolibrary.org/obo/OBI_0500014 Study Design Type Term Source REF OBI OBI STUDY PUBLICATIONS Study PubMed ID 23587118 Study Publication DOI 10.1186/2047-217X-1-18 Study Publication Author List Ruibang Luo et al. Study Publication Title SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Study Publication Status published Study Publication Status Term Accession Number Study Publication Status Term Source REF STUDY FACTORS Study Factor Name sequence assembly algorithm genome size Study Factor Type sequence assembly algorithm size Study Factor Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0001522 http://purl.obolibrary.org/obo/PATO_0000117 Study Factor Type Term Source REF OBI PATO STUDY ASSAYS Study Assay File Name a_assay_soapdenovo2.txt Study Assay Measurement Type genome sequencing Study Assay Measurement Type Term Accession Number Study Assay Measurement Type Term Source REF Study Assay Technology Type nucleotide sequencing Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 Study Assay Technology Type Term Source REF OBI Study Assay Technology Platform STUDY PROTOCOLS Study Protocol Name sample collection soapdenovo2-sequence assembly soapdenovo1-sequence assembly ALLPATHS-LG-sequence assembly soapdenovo1-h-sapiens-sequence assembly soapdenovo2-h-sapiens-sequence assembly ALLPATH-LG-h-sapiens-sequence assembly soapdenovo1-b-impatiens-sequence assembly soapdenovo2-b-impatiens-sequence assembly ALLPATH-LG-b-impatiens-sequence assembly soapdenovo1-s-aureus-sequence assembly soapdenovo2-s-aureus-sequence assembly ALLPATH-LG-s-aureus-sequence assembly soapdenovo1-r-sphaeroides-sequence assembly soapdenovo2-r-sphaeroides-sequence assembly ALLPATH-LG-r-sphaeroides-sequence assembly sequence assembly nucleic acid extraction library construction nucleic acid sequencing data download mock extraction mock library construction mock sequencing nanopublicationStudy Protocol Type specimen collection sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process sequence assembly process nucleic acid extraction library preparation nucleic acid sequencing information acquisition nucleic acid extraction library preparation nucleic acid sequencing data transformationStudy Protocol Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000659 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0001872 http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/OBI_0000711 http://purl.obolibrary.org/obo/OBI_0600013 http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/OBI_0000711 http://purl.obolibrary.org/obo/OBI_0200000Study Protocol Type Term Source REF OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBI OBIStudy Protocol Description Study Protocol URI http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-soapdenovo1 http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2 http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-s-aureus-genome-assembly-using-allpaths http://gigagalaxy.net/u/peterli/w/workflow-constructed-from-history-r-sphaeroides-genome-assembly-using-soapdenovo1 http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-soapdenovo2 http://gigagalaxy.net/u/peterli/w/assembling-the-r-sphaeroides-genome-using-allpaths http://dx.doi.org/10.5524/100044 Study Protocol Version Study Protocol Parameters Name software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url software location;sequence assembly algorithm;software script;workflow url library selection;library layout;library strategy;library source base caller;quality scorer;sequencing instrument Study Protocol Parameters Name Term Accession Number ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;; Study Protocol Parameters Name Term Source REF ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;;; ;; Study Protocol Components Name Study Protocol Components Type Study Protocol Components Type Term Accession Number Study Protocol Components Type Term Source REF STUDY CONTACTS Study Person Last Name Edmunds Luo Lam Li Gonzalez-Beltran Rocca-Serra Study Person First Name Scott Ruibang Tak-Wah Peter Alejandra Philippe Study Person Mid Initials Study Person Email [email protected] [email protected] [email protected] [email protected] [email protected] Study Person Phone Study Person Fax Study Person Address "Shenzhen,China" "Shenzhen, China" Hong Kong "Shenzhen,China" University of Oxford University of Oxford Study Person Affiliation Gigascience Beigjing Genome Institute "HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong," Gigascience Oxford e-Research Centre Oxford e-Research Centre Study Person Roles journal editor data producer data producer responsible for Galaxy workflows "software architect responsible for ISA-TAB creation, conversion to RDF and nanopublication" "data manager responsible for ISA-TAB creation, conversion to RDF and nanopublication" Study Person Roles Term Accession Number Study Person Roles Term Source REF Comment[Study Person REF] http://orcid.org/0000-0001-6444-1436 http://orcid.org/0000-0001-9711-6533 http://orcid.org/0000-0003-4676-8587 http://orcid.org/0000-0001-9602-9550 http://orcid.org/0000-0003-3499-8262 http://orcid.org/0000-0001-9853-5668