{"id":"https://openalex.org/W4417164599","doi":"https://doi.org/10.1186/s12859-025-06343-6","title":"SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data","display_name":"SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data","publication_year":2025,"publication_date":"2025-12-09","ids":{"openalex":"https://openalex.org/W4417164599","doi":"https://doi.org/10.1186/s12859-025-06343-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41366728"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06343-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06343-6","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://doi.org/10.1186/s12859-025-06343-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101418402","display_name":"Jie Kang","orcid":"https://orcid.org/0000-0002-9619-5775"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I141766778","display_name":"Teagasc - The Irish Agriculture and Food Development Authority","ror":"https://ror.org/03sx84n71","country_code":"IE","type":"facility","lineage":["https://openalex.org/I141766778"]},{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["AU","IE","NZ"],"is_corresponding":false,"raw_author_name":"Jie Kang","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney, Sydney, Australia","Crops Research Centre, Teagasc, Oak Park, Carlow, Ireland","Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-9619-5775","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney, Sydney, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Crops Research Centre, Teagasc, Oak Park, Carlow, Ireland","institution_ids":["https://openalex.org/I141766778"]},{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026907215","display_name":"Melanie K. Hess","orcid":"https://orcid.org/0000-0002-7502-0036"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]},{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ","US"],"is_corresponding":false,"raw_author_name":"Melanie K. Hess","raw_affiliation_strings":["Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","University of Nebraska-Lincoln, Lincoln, USA"],"raw_orcid":"https://orcid.org/0000-0002-7502-0036","affiliations":[{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]},{"raw_affiliation_string":"University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058921217","display_name":"K. G. Dodds","orcid":"https://orcid.org/0000-0002-9347-6379"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Ken G. Dodds","raw_affiliation_strings":["Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-9347-6379","affiliations":[{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030305018","display_name":"R\u00fcdiger Br\u00e4uning","orcid":"https://orcid.org/0000-0001-5068-9166"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Rudiger Brauning","raw_affiliation_strings":["Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand"],"raw_orcid":"https://orcid.org/0000-0001-5068-9166","affiliations":[{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002736526","display_name":"John C. McEwan","orcid":"https://orcid.org/0000-0003-4801-6207"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"John C. McEwan","raw_affiliation_strings":["Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand"],"raw_orcid":"https://orcid.org/0000-0003-4801-6207","affiliations":[{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111909714","display_name":"BJ Foote","orcid":null},"institutions":[{"id":"https://openalex.org/I1302741095","display_name":"Statistics New Zealand","ror":"https://ror.org/055qjgz33","country_code":"NZ","type":"government","lineage":["https://openalex.org/I1302741095","https://openalex.org/I2802073567"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Barry J. Foote","raw_affiliation_strings":[", Hikurangi, New Zealand, 859 Russell Road, 0184","Hikurangi, New Zealand, 859 Russell Road, 0184"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":", Hikurangi, New Zealand, 859 Russell Road, 0184","institution_ids":["https://openalex.org/I1302741095"]},{"raw_affiliation_string":"Hikurangi, New Zealand, 859 Russell Road, 0184","institution_ids":["https://openalex.org/I1302741095"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109204313","display_name":"Judy F. Foote","orcid":null},"institutions":[{"id":"https://openalex.org/I1302741095","display_name":"Statistics New Zealand","ror":"https://ror.org/055qjgz33","country_code":"NZ","type":"government","lineage":["https://openalex.org/I1302741095","https://openalex.org/I2802073567"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Judy F. Foote","raw_affiliation_strings":[", Hikurangi, New Zealand, 859 Russell Road, 0184","Hikurangi, New Zealand, 859 Russell Road, 0184"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":", Hikurangi, New Zealand, 859 Russell Road, 0184","institution_ids":["https://openalex.org/I1302741095"]},{"raw_affiliation_string":"Hikurangi, New Zealand, 859 Russell Road, 0184","institution_ids":["https://openalex.org/I1302741095"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Agnieszka Konkolewska","orcid":"https://orcid.org/0000-0003-3030-9319"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I141766778","display_name":"Teagasc - The Irish Agriculture and Food Development Authority","ror":"https://ror.org/03sx84n71","country_code":"IE","type":"facility","lineage":["https://openalex.org/I141766778"]},{"id":"https://openalex.org/I2800693937","display_name":"Bon Secours Hospital Cork","ror":"https://ror.org/0197t7j38","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I160713005","https://openalex.org/I2800693937"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Agnieszka Konkolewska","raw_affiliation_strings":["Crops Research Centre, Teagasc, Oak Park, Carlow, Ireland","Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin 4, Ireland","VistaMilk SFI Research Centre, Moorepark, Fermoy, Co. Cork, Ireland"],"raw_orcid":"https://orcid.org/0000-0003-3030-9319","affiliations":[{"raw_affiliation_string":"Crops Research Centre, Teagasc, Oak Park, Carlow, Ireland","institution_ids":["https://openalex.org/I141766778"]},{"raw_affiliation_string":"Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"VistaMilk SFI Research Centre, Moorepark, Fermoy, Co. Cork, Ireland","institution_ids":["https://openalex.org/I2800693937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002400154","display_name":"Shannon Clarke","orcid":"https://orcid.org/0000-0002-4615-8917"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Shannon M. Clarke","raw_affiliation_strings":["Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand. Shannon.Clarke@agresearch.co.nz","Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-4615-8917","affiliations":[{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand. Shannon.Clarke@agresearch.co.nz","institution_ids":["https://openalex.org/I41125697"]},{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046569227","display_name":"Andrew S. Hess","orcid":"https://orcid.org/0000-0001-6738-3817"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]},{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ","US"],"is_corresponding":true,"raw_author_name":"Andrew S. Hess","raw_affiliation_strings":["Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, USA. ahess@unr.edu","Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand. ahess@unr.edu","Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, USA"],"raw_orcid":"https://orcid.org/0000-0001-6738-3817","affiliations":[{"raw_affiliation_string":"Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, USA. ahess@unr.edu","institution_ids":["https://openalex.org/I134113660"]},{"raw_affiliation_string":"Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand. ahess@unr.edu","institution_ids":["https://openalex.org/I41125697"]},{"raw_affiliation_string":"Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, USA","institution_ids":["https://openalex.org/I134113660"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5002400154","https://openalex.org/A5046569227"],"corresponding_institution_ids":["https://openalex.org/I134113660","https://openalex.org/I41125697"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.893,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.80627538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"27","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.8033000230789185,"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"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.8033000230789185,"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"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.06360000371932983,"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"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.03999999910593033,"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/benchmark","display_name":"Benchmark (surveying)","score":0.6434000134468079},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5889000296592712},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5228000283241272},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4366999864578247},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.3718000054359436},{"id":"https://openalex.org/keywords/linkage","display_name":"Linkage (software)","score":0.3686000108718872},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.35280001163482666}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6434000134468079},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.631600022315979},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5889000296592712},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5415999889373779},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5228000283241272},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4366999864578247},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37389999628067017},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.3718000054359436},{"id":"https://openalex.org/C31266012","wikidata":"https://www.wikidata.org/wiki/Q6554340","display_name":"Linkage (software)","level":3,"score":0.3686000108718872},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.35280001163482666},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33390000462532043},{"id":"https://openalex.org/C37463918","wikidata":"https://www.wikidata.org/wiki/Q387981","display_name":"Allele frequency","level":4,"score":0.3301999866962433},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.27059999108314514},{"id":"https://openalex.org/C161890455","wikidata":"https://www.wikidata.org/wiki/Q1503548","display_name":"Heritability","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.2605000138282776}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06343-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06343-6","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41366728","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41366728","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":"Journal Article"},{"id":"pmh:oai:doaj.org/article:66a08564e0b84e1590b816b5f4697ce4","is_oa":true,"landing_page_url":"https://doaj.org/article/66a08564e0b84e1590b816b5f4697ce4","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 27, Iss 1, Pp 1-20 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12801997","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12801997/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06343-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06343-6","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W790336629","https://openalex.org/W1972216668","https://openalex.org/W1978150238","https://openalex.org/W1999245186","https://openalex.org/W2036897871","https://openalex.org/W2053657447","https://openalex.org/W2053755275","https://openalex.org/W2068974951","https://openalex.org/W2085222782","https://openalex.org/W2085315239","https://openalex.org/W2110597285","https://openalex.org/W2111242966","https://openalex.org/W2113896673","https://openalex.org/W2117608012","https://openalex.org/W2119923823","https://openalex.org/W2124146565","https://openalex.org/W2126927236","https://openalex.org/W2129034036","https://openalex.org/W2131112579","https://openalex.org/W2150131459","https://openalex.org/W2159474015","https://openalex.org/W2170551349","https://openalex.org/W2193546062","https://openalex.org/W2412288472","https://openalex.org/W2467325308","https://openalex.org/W2514359199","https://openalex.org/W2561707810","https://openalex.org/W2594081754","https://openalex.org/W2772422534","https://openalex.org/W2783281640","https://openalex.org/W2790559169","https://openalex.org/W2949930656","https://openalex.org/W2952119783","https://openalex.org/W3007506343","https://openalex.org/W3015573894","https://openalex.org/W3028465858","https://openalex.org/W3118936113","https://openalex.org/W4246764585","https://openalex.org/W6922495979"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Genotyping-by-sequencing":[1],"(GBS)":[2],"offers":[3],"a":[4,49,100,123,168,175,244],"cost-effective":[5,50],"solution":[6],"to":[7,52,69,91,103,177,247],"access":[8],"genomic":[9,22],"information":[10],"on":[11,95],"many":[12,40],"samples.":[13],"The":[14,208],"advent":[15],"of":[16,30,72,171,190,214,219],"GBS":[17,44,128,182,239,251,261],"has":[18],"promoted":[19],"large":[20,265],"scale":[21,266],"analyses,":[23],"including":[24,187],"linkage":[25],"analysis,":[26],"heritability":[27],"estimation,":[28],"inference":[29],"genetic":[31],"relatedness":[32],"and":[33,36,93,107,115,193,202,257],"genome-wide":[34],"prediction":[35],"association":[37],"studies,":[38],"in":[39,142,205,237,264],"non-model":[41],"species.":[42],"Low-depth":[43],"can":[45,67,88,145,156],"be":[46,60,89,147],"used":[47],"as":[48],"method":[51,118,124,209],"obtain":[53],"genotypes;":[54],"however,":[55],"not":[56],"all":[57],"alleles":[58],"will":[59],"captured":[61],"during":[62],"the":[63,152,188,234],"sequencing":[64,194],"process,":[65],"which":[66],"lead":[68],"high":[70],"levels":[71],"genotype":[73,79,200],"uncertainty.":[74],"New":[75],"methods":[76,87,114,259],"that":[77],"take":[78],"uncertainty":[80],"into":[81],"account":[82],"are":[83,109,184],"needed,":[84],"but":[85,144],"these":[86],"difficult":[90],"develop":[92],"benchmark":[94,104],"real":[96,132],"data.":[97,240],"Simulations":[98],"provide":[99],"convenient":[101],"way":[102],"different":[105],"approaches,":[106],"therefore,":[108],"essential":[110],"for":[111,125,217,221,260],"assessing":[112],"existing":[113],"guiding":[116],"future":[117],"development.":[119],"RESULTS:":[120],"SimGBS":[121,196,242],"is":[122,140,210,243],"simulating":[126,223],"large-scale":[127],"data":[129,262],"from":[130,149],"any":[131],"(e.g.,":[133],"reference)":[134],"or":[135,173,253],"simulated":[136],"diploid":[137],"genome.":[138],"It":[139],"implemented":[141],"Julia":[143],"also":[146],"accessed":[148],"R":[150],"through":[151],"JuliaCall":[153],"interface.":[154],"Users":[155],"define":[157],"populations":[158],"with":[159,249],"distinct":[160],"demographic":[161],"histories":[162],"by":[163],"modifying":[164],"population":[165,267],"size":[166],"over":[167],"specified":[169],"number":[170],"generations":[172],"providing":[174],"pedigree":[176],"generate":[178],"structured":[179],"populations.":[180],"Most":[181],"parameters":[183],"highly":[185],"customisable,":[186],"choice":[189],"restriction":[191],"enzyme":[192],"depth.":[195],"outputs":[197],"both":[198],"true":[199],"calls":[201],"DNA":[203],"sequences":[204],"FASTQ":[206],"format.":[207],"computationally":[211],"efficient,":[212],"capable":[213],"generating":[215],"datasets":[216],"thousands":[218],"individuals;":[220],"example,":[222],"172":[224],"samples":[225],"required":[226],"less":[227],"than":[228],"two":[229],"hours":[230],"while":[231],"successfully":[232],"reproducing":[233],"complexities":[235],"observed":[236],"empirical":[238],"CONCLUSION:":[241],"valuable":[245],"tool":[246],"assist":[248],"designing":[250],"experiments":[252],"evaluating":[254],"bioinformatic":[255],"pipelines":[256],"statistical":[258],"analysis":[263],"genetics":[268],"studies.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-12-09T00:00:00"}
