{"id":"https://openalex.org/W2619546318","doi":"https://doi.org/10.1186/s12859-017-1690-0","title":"Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities","display_name":"Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities","publication_year":2017,"publication_date":"2017-05-30","ids":{"openalex":"https://openalex.org/W2619546318","doi":"https://doi.org/10.1186/s12859-017-1690-0","mag":"2619546318","pmid":"https://pubmed.ncbi.nlm.nih.gov/28558684"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1690-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1690-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1690-0","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/s12859-017-1690-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063888317","display_name":"Jonathan L. Golob","orcid":"https://orcid.org/0000-0003-0009-5815"},"institutions":[{"id":"https://openalex.org/I1330732676","display_name":"Infectious Disease Research Institute","ror":"https://ror.org/03y4myd35","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1330732676"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan L. Golob","raw_affiliation_strings":["Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA. jgolob@fredhutch.org","Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA. jgolob@fredhutch.org","Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA. jgolob@fredhutch.org","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA. jgolob@fredhutch.org","institution_ids":["https://openalex.org/I1330732676"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041725535","display_name":"Elisa Margolis","orcid":"https://orcid.org/0000-0001-6217-0564"},"institutions":[{"id":"https://openalex.org/I1295499534","display_name":"Seattle Children's Hospital","ror":"https://ror.org/01njes783","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1295499534"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elisa Margolis","raw_affiliation_strings":["Seattle Childrens Hospital, Seattle, WA, USA","Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Seattle Childrens Hospital, Seattle, WA, USA","institution_ids":["https://openalex.org/I1295499534"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008533836","display_name":"Noah G. Hoffman","orcid":"https://orcid.org/0000-0001-6791-7727"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah G. Hoffman","raw_affiliation_strings":["Department Laboratory Medicine, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department Laboratory Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008191792","display_name":"David N. Fredricks","orcid":"https://orcid.org/0000-0003-2735-6800"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David N. Fredricks","raw_affiliation_strings":["Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA","Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5063888317"],"corresponding_institution_ids":["https://openalex.org/I1330732676","https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":4.6608,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.96031529,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"283","last_page":"283"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.98580002784729,"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"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.98580002784729,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0026000000070780516,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.002099999925121665,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/unifrac","display_name":"UniFrac","score":0.8178742527961731},{"id":"https://openalex.org/keywords/operational-taxonomic-unit","display_name":"Operational taxonomic unit","score":0.7933415174484253},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.6945493221282959},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.6038047671318054},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5398302674293518},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5121128559112549},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5017900466918945},{"id":"https://openalex.org/keywords/amplicon-sequencing","display_name":"Amplicon sequencing","score":0.48844805359840393},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.48771652579307556},{"id":"https://openalex.org/keywords/alpha-diversity","display_name":"Alpha diversity","score":0.48236602544784546},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47634604573249817},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4542336165904999},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.44271180033683777},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"Human microbiome","score":0.4268138110637665},{"id":"https://openalex.org/keywords/taxonomic-rank","display_name":"Taxonomic rank","score":0.42354440689086914},{"id":"https://openalex.org/keywords/16s-ribosomal-rna","display_name":"16S ribosomal RNA","score":0.38830721378326416},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.387581467628479},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38048332929611206},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.31558603048324585},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.20845842361450195},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18656378984451294},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.147273987531662},{"id":"https://openalex.org/keywords/species-diversity","display_name":"Species diversity","score":0.12678778171539307},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.1239616870880127}],"concepts":[{"id":"https://openalex.org/C151437367","wikidata":"https://www.wikidata.org/wiki/Q7884646","display_name":"UniFrac","level":4,"score":0.8178742527961731},{"id":"https://openalex.org/C2779825944","wikidata":"https://www.wikidata.org/wiki/Q7097792","display_name":"Operational taxonomic unit","level":4,"score":0.7933415174484253},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6945493221282959},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.6038047671318054},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5398302674293518},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5121128559112549},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5017900466918945},{"id":"https://openalex.org/C2993206177","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon sequencing","level":4,"score":0.48844805359840393},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.48771652579307556},{"id":"https://openalex.org/C23913935","wikidata":"https://www.wikidata.org/wiki/Q2650881","display_name":"Alpha diversity","level":3,"score":0.48236602544784546},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47634604573249817},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4542336165904999},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.44271180033683777},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.4268138110637665},{"id":"https://openalex.org/C189592816","wikidata":"https://www.wikidata.org/wiki/Q427626","display_name":"Taxonomic rank","level":3,"score":0.42354440689086914},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.38830721378326416},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.387581467628479},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38048332929611206},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.31558603048324585},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.20845842361450195},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18656378984451294},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.147273987531662},{"id":"https://openalex.org/C62648534","wikidata":"https://www.wikidata.org/wiki/Q706937","display_name":"Species diversity","level":2,"score":0.12678778171539307},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.1239616870880127},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007422","descriptor_name":"Intestines","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D007422","descriptor_name":"Intestines","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D007422","descriptor_name":"Intestines","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-017-1690-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1690-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1690-0","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:28558684","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28558684","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:europepmc.org:4306136","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC5450146","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5450146","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5450146","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:7330e6e9d7a44eaeba9da5da3cc49852","is_oa":true,"landing_page_url":"https://doaj.org/article/7330e6e9d7a44eaeba9da5da3cc49852","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1690-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1690-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1690-0","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":[],"awards":[{"id":"https://openalex.org/G105350897","display_name":null,"funder_award_id":"T32AI118690","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1084746053","display_name":"FHCRC High-Performance Computing Cluster","funder_award_id":"1s10od020069-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G172982731","display_name":null,"funder_award_id":"T32 AI007044","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2619546318.pdf","grobid_xml":"https://content.openalex.org/works/W2619546318.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1545338289","https://openalex.org/W1971536609","https://openalex.org/W1988925586","https://openalex.org/W1995875735","https://openalex.org/W2022111190","https://openalex.org/W2032678548","https://openalex.org/W2034285706","https://openalex.org/W2056279562","https://openalex.org/W2059237622","https://openalex.org/W2072970694","https://openalex.org/W2074084106","https://openalex.org/W2099117570","https://openalex.org/W2103412200","https://openalex.org/W2103923544","https://openalex.org/W2104318549","https://openalex.org/W2108718991","https://openalex.org/W2113925621","https://openalex.org/W2115701239","https://openalex.org/W2124351063","https://openalex.org/W2125230147","https://openalex.org/W2130075028","https://openalex.org/W2136879569","https://openalex.org/W2136993578","https://openalex.org/W2141034720","https://openalex.org/W2156619206","https://openalex.org/W2157539385","https://openalex.org/W2160209604","https://openalex.org/W2170024099","https://openalex.org/W2239696860","https://openalex.org/W2404548783","https://openalex.org/W2506843120","https://openalex.org/W2553548418","https://openalex.org/W2950912511","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2067166176","https://openalex.org/W3191349168","https://openalex.org/W4281820523","https://openalex.org/W2949680881","https://openalex.org/W4299855273","https://openalex.org/W4213427769","https://openalex.org/W2120878769","https://openalex.org/W4380264664","https://openalex.org/W3175210068","https://openalex.org/W4255734824"],"abstract_inverted_index":{"BACKGROUND:":[0],"Microbiome":[1],"studies":[2],"commonly":[3],"use":[4],"16S":[5],"rRNA":[6],"gene":[7],"amplicon":[8],"sequencing":[9],"to":[10,75,123,136,310],"characterize":[11],"microbial":[12],"communities.":[13],"Errors":[14],"introduced":[15,195],"at":[16],"multiple":[17],"steps":[18],"in":[19,49,196,204,212,254,294],"this":[20],"process":[21],"can":[22,235,313],"affect":[23],"the":[24,27,32,83,95,115,205,209,220,224,241,258,261,267,295,316,322],"interpretation":[25],"of":[26,34,86,99,114,138,144,149,243,260,273,298],"data.":[28],"Here":[29],"we":[30,65],"evaluate":[31,304],"accuracy":[33,158,176,242,259],"operational":[35],"taxonomic":[36,40,106,244],"unit":[37],"(OTU)":[38],"generation,":[39],"classification,":[41,245],"alpha-":[42,247],"and":[43,52,97,152,170,230,246,248,287,308],"beta-diversity":[44,249],"measures":[45],"for":[46,81,111],"different":[47],"settings":[48,154,202,255,309,326],"QIIME,":[50],"MOTHUR":[51],"a":[53,58,79,237,275],"pplacer-based":[54],"classification":[55,107,126,222],"pipeline,":[56,223],"using":[57,219],"novel":[59],"software":[60,171,289],"package:":[61],"DECARD.":[62],"RESULTS:":[63],"In-silico":[64],"generated":[66],"100":[67],"synthetic":[68,91],"bacterial":[69],"communities":[70],"approximating":[71],"human":[72,102],"stool":[73,103],"microbiomes":[74],"be":[76,292,328],"used":[77,278],"as":[78],"gold-standard":[80],"evaluating":[82],"colligative":[84],"performance":[85],"microbiome":[87,300],"analysis":[88,232],"software.":[89],"Our":[90],"data":[92],"closely":[93],"matched":[94],"composition":[96],"complexity":[98],"actual":[100],"healthy":[101],"microbiomes.":[104],"Genus-level":[105],"was":[108,127],"correctly":[109],"done":[110],"only":[112],"50.4-74.8%":[113],"source":[116],"organisms.":[117],"Miscall":[118],"rates":[119,133],"varied":[120,146,159],"from":[121,266],"11.9":[122],"23.5%.":[124],"Species-level":[125],"less":[128],"successful,":[129],"(6.9-18.9%":[130],"correct);":[131],"miscall":[132,145],"were":[134,190,207],"comparable":[135],"those":[137],"genus-level":[139],"targets":[140],"(12.5-26.2%).":[141],"The":[142,201],"degree":[143],"by":[147,160],"clade":[148],"organism,":[150],"pipeline":[151,276,307],"specific":[153,225,271,288],"used.":[155],"OTU":[156,280],"generation":[157,281],"strategy":[161],"(closed,":[162],"de":[163],"novo":[164],"or":[165,324,330],"subsampling),":[166],"reference":[167,228,283],"database,":[168],"algorithm":[169,286],"implementation.":[172],"Shannon":[173],"diversity":[174],"estimation":[175],"correlated":[177],"generally":[178],"with":[179,184],"OTU-generation":[180,226],"accuracy.":[181],"Beta-diversity":[182],"estimates":[183],"Double":[185],"Principle":[186],"Coordinate":[187],"Analysis":[188],"(DPCoA)":[189],"more":[191],"robust":[192],"against":[193],"errors":[194],"processing":[197],"than":[198,320],"Weighted":[199],"UniFrac.":[200],"suggested":[203],"tutorials":[206],"among":[208],"worst":[210],"performing":[211],"all":[213,299],"outcomes":[214],"tested.":[215],"CONCLUSIONS:":[216],"Even":[217,251],"when":[218],"same":[221],"strategy,":[227,282],"database":[229],"downstream":[231],"methods":[233,296],"selection":[234],"have":[236],"dramatic":[238],"effect":[239],"on":[240],"estimation.":[250],"minor":[252],"changes":[253],"adversely":[256],"affected":[257],"results,":[262],"bringing":[263],"them":[264],"far":[265],"best-observed":[268],"result.":[269],"Thus,":[270],"details":[272],"how":[274],"is":[277],"(including":[279],"sets,":[284],"clustering":[285],"implementation)":[290],"should":[291,303],"specified":[293],"section":[297],"studies.":[301],"Researchers":[302],"their":[305],"chosen":[306],"confirm":[311],"it":[312],"adequately":[314],"answer":[315],"research":[317],"question":[318],"rather":[319],"assuming":[321],"tutorial":[323],"standard-operating-procedure":[325],"will":[327],"adequate":[329],"optimal.":[331]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-15T07:11:24.734988","created_date":"2025-10-10T00:00:00"}
