{"id":"https://openalex.org/W2777994090","doi":"https://doi.org/10.1186/s12859-017-2000-6","title":"A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy","display_name":"A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2777994090","doi":"https://doi.org/10.1186/s12859-017-2000-6","mag":"2777994090","pmid":"https://pubmed.ncbi.nlm.nih.gov/29281959"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-2000-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-2000-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-2000-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-2000-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078581248","display_name":"Daniel P. Wickland","orcid":"https://orcid.org/0000-0001-5313-6276"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel P. Wickland","raw_affiliation_strings":["Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083675871","display_name":"Gopal Battu","orcid":"https://orcid.org/0000-0002-3042-6518"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210145894","display_name":"HudsonAlpha Institute for Biotechnology","ror":"https://ror.org/04nz0wq19","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210145894"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gopal Battu","raw_affiliation_strings":["Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","HudsonAlpha Institute for Biotechnology, 601 Genome Way, NW, Huntsville, AL, 35806, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"HudsonAlpha Institute for Biotechnology, 601 Genome Way, NW, Huntsville, AL, 35806, USA","institution_ids":["https://openalex.org/I4210145894"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057849386","display_name":"Karen A. Hudson","orcid":"https://orcid.org/0000-0002-7402-2275"},"institutions":[{"id":"https://openalex.org/I159548981","display_name":"State Street (United States)","ror":"https://ror.org/0116zdb24","country_code":"US","type":"company","lineage":["https://openalex.org/I159548981"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen A. Hudson","raw_affiliation_strings":["USDA-ARS Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN, 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USDA-ARS Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN, 47907, USA","institution_ids":["https://openalex.org/I159548981"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047366274","display_name":"Brian W. Diers","orcid":"https://orcid.org/0000-0003-3584-5495"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian W. Diers","raw_affiliation_strings":["Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024496701","display_name":"Matthew E. Hudson","orcid":"https://orcid.org/0000-0002-4737-0936"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew E. Hudson","raw_affiliation_strings":["Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. mhudson@illinois.edu","Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. mhudson@illinois.edu","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":10.6359,"has_fulltext":true,"cited_by_count":84,"citation_normalized_percentile":{"value":0.97748467,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"586","last_page":"586"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12571","display_name":"Soybean genetics and cultivation","score":0.29660001397132874,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12571","display_name":"Soybean genetics and cultivation","score":0.29660001397132874,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.16089999675750732,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.1062999963760376,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5602791905403137},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5515183210372925},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.5510823130607605},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5433486104011536},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4938831925392151},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46817249059677124},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4448947310447693},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39356666803359985},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35963380336761475},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3387943506240845},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.25927895307540894},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12123402953147888},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11467421054840088}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5602791905403137},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5515183210372925},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.5510823130607605},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5433486104011536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4938831925392151},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46817249059677124},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4448947310447693},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39356666803359985},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35963380336761475},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3387943506240845},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.25927895307540894},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12123402953147888},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11467421054840088}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-2000-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-2000-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-2000-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29281959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29281959","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:46b3372ef31a43f9b5825dd63b520386","is_oa":true,"landing_page_url":"https://doaj.org/article/46b3372ef31a43f9b5825dd63b520386","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss 1, Pp 1-12 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4665405","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5745977","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-2000-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-2000-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-2000-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320316793","display_name":"North Central Soybean Research Program","ror":null},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2777994090.pdf","grobid_xml":"https://content.openalex.org/works/W2777994090.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1485543081","https://openalex.org/W1972216668","https://openalex.org/W1984968452","https://openalex.org/W2012986985","https://openalex.org/W2036897871","https://openalex.org/W2039233269","https://openalex.org/W2042346872","https://openalex.org/W2044534398","https://openalex.org/W2060965924","https://openalex.org/W2075570000","https://openalex.org/W2095680943","https://openalex.org/W2095882149","https://openalex.org/W2103441770","https://openalex.org/W2107628071","https://openalex.org/W2108524369","https://openalex.org/W2110035718","https://openalex.org/W2112484080","https://openalex.org/W2119180969","https://openalex.org/W2124465358","https://openalex.org/W2131112579","https://openalex.org/W2140067143","https://openalex.org/W2149992227","https://openalex.org/W2150131459","https://openalex.org/W2159474015","https://openalex.org/W2163659174","https://openalex.org/W2169773990","https://openalex.org/W2190569576","https://openalex.org/W2269415044","https://openalex.org/W2292610840","https://openalex.org/W2509491391","https://openalex.org/W2514269399","https://openalex.org/W2529596433","https://openalex.org/W2561707810","https://openalex.org/W2607746504","https://openalex.org/W2906926620","https://openalex.org/W2951808978"],"related_works":["https://openalex.org/W2378369506","https://openalex.org/W2030447374","https://openalex.org/W2353370357","https://openalex.org/W2806032235","https://openalex.org/W2755824586","https://openalex.org/W4280553679","https://openalex.org/W4212927541","https://openalex.org/W2975902501","https://openalex.org/W4248994802","https://openalex.org/W2160549327"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genotyping-by-sequencing":[1],"(GBS),":[2],"a":[3,85,89,130,306],"method":[4,37],"to":[5,20,143,154,254,288,322],"identify":[6],"genetic":[7],"variants":[8],"and":[9,42,56,64,98,141,147,160,234,263,282,290],"quickly":[10],"genotype":[11],"samples,":[12],"reduces":[13],"genome":[14,23],"complexity":[15],"by":[16,75],"using":[17,111],"restriction":[18],"enzymes":[19],"divide":[21],"the":[22,67,105,145,163,197,209,231,260,299,310,319,324],"into":[24],"fragments":[25],"whose":[26],"ends":[27],"are":[28,279],"sequenced":[29],"on":[30,52,83,208,243,298],"short-read":[31],"sequencing":[32,175],"platforms.":[33],"While":[34,292],"cost-effective,":[35],"this":[36],"produces":[38],"extensive":[39],"missing":[40,235],"data":[41,97,115,151,211,236,246],"requires":[43],"complex":[44],"bioinformatics":[45,132,315],"analysis.":[46,152],"GBS":[47,70,96,109,131,150,156,182,314],"is":[48,218,270],"most":[49,326],"commonly":[50,283],"used":[51,137],"crop":[53,58,87],"plant":[54],"genomes,":[55],"because":[57],"plants":[59],"have":[60],"highly":[61,90,327],"variable":[62],"ploidy":[63],"repeat":[65],"content,":[66],"performance":[68,106],"of":[69,107,149,166,176,204,238,259],"analysis":[71,82,183],"software":[72,228,276],"can":[73],"vary":[74],"target":[76],"organism.":[77],"Here":[78],"we":[79,127],"focus":[80],"our":[81,302],"soybean,":[84],"polyploid":[86,334],"with":[88,124,168,173],"duplicated":[91],"genome,":[92],"relatively":[93],"little":[94],"public":[95],"few":[99],"dedicated":[100],"tools.":[101],"RESULTS:":[102],"We":[103,214],"compared":[104],"five":[108,181],"pipelines":[110,316],"low-coverage":[112,210,244,333],"Illumina":[113],"sequence":[114,335],"from":[116,247,272,312,332],"three":[117],"soybean":[118],"populations.":[119],"To":[120],"address":[121],"issues":[122],"identified":[123,162],"existing":[125,273],"methods,":[126],"developed":[128],"GB-eaSy,":[129],"workflow":[133],"that":[134,196,216,278,305],"incorporates":[135],"widely":[136],"genomics":[138],"tools,":[139],"parallelization":[140],"automation":[142],"increase":[144],"accuracy":[146],"accessibility":[148],"Compared":[153],"other":[155,226,255,295],"pipelines,":[157],"GB-eaSy":[158,217,269,293],"rapidly":[159],"accurately":[161],"greatest":[164],"number":[165],"SNPs,":[167],"SNP":[169,185,206,329],"calls":[170,186,207],"closely":[171],"concordant":[172],"whole-genome":[174],"selected":[177],"lines.":[178],"Across":[179],"all":[180],"platforms,":[184],"showed":[187],"unexpectedly":[188],"low":[189],"convergence":[190],"but":[191],"generally":[192],"high":[193],"accuracy,":[194,232],"indicating":[195],"workflows":[198],"arrived":[199],"at":[200],"largely":[201],"complementary":[202],"sets":[203],"valid":[205],"analyzed.":[212],"CONCLUSIONS:":[213],"show":[215],"approximately":[219],"as":[220,241],"good":[221],"as,":[222],"or":[223],"better":[224],"than,":[225],"leading":[227],"solutions":[229,256],"in":[230,257],"yield":[233,330],"fraction":[237],"variant":[239],"calling,":[240],"tested":[242],"genomic":[245],"soybean.":[248],"It":[249],"also":[250],"performs":[251],"well":[252],"relative":[253],"terms":[258],"run":[261],"time":[262],"disk":[264],"space":[265],"required.":[266],"In":[267],"addition,":[268],"built":[271],"open-source,":[274],"modular":[275],"packages":[277],"regularly":[280],"updated":[281],"used,":[284],"making":[285],"it":[286],"straightforward":[287],"install":[289],"maintain.":[291],"outperformed":[294],"individual":[296],"methods":[297],"datasets":[300],"analyzed,":[301],"findings":[303],"suggest":[304],"comprehensive":[307],"approach":[308],"integrating":[309],"results":[311],"multiple":[313],"may":[317],"be":[318],"optimal":[320],"strategy":[321],"obtain":[323],"largest,":[325],"accurate":[328],"possible":[331],"data.":[336]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}