{"id":"https://openalex.org/W2898222896","doi":"https://doi.org/10.1093/bioinformatics/bty901","title":"Flexible design of multiple metagenomics classification pipelines with UGENE","display_name":"Flexible design of multiple metagenomics classification pipelines with UGENE","publication_year":2018,"publication_date":"2018-10-25","ids":{"openalex":"https://openalex.org/W2898222896","doi":"https://doi.org/10.1093/bioinformatics/bty901","mag":"2898222896","pmid":"https://pubmed.ncbi.nlm.nih.gov/30358807"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty901","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty901","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1963/28759282/bty901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1963/28759282/bty901.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002919205","display_name":"Rebecca Rose","orcid":"https://orcid.org/0000-0002-7711-2209"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rebecca Rose","raw_affiliation_strings":["BioInfoExperts, LLC, Thibodaux, LA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioInfoExperts, LLC, Thibodaux, LA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029978860","display_name":"Olga Golosova","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Olga Golosova","raw_affiliation_strings":["UNIPRO, LLC, Novosibirsk, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UNIPRO, LLC, Novosibirsk, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014613715","display_name":"Dmitrii Sukhomlinov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dmitrii Sukhomlinov","raw_affiliation_strings":["UNIPRO, LLC, Novosibirsk, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UNIPRO, LLC, Novosibirsk, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013186801","display_name":"A. Tiunov","orcid":"https://orcid.org/0000-0003-2015-8828"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aleksey Tiunov","raw_affiliation_strings":["UNIPRO, LLC, Novosibirsk, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UNIPRO, LLC, Novosibirsk, Russia","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039419132","display_name":"Mattia Prosperi","orcid":"https://orcid.org/0000-0002-9021-5595"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mattia Prosperi","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5029978860","https://openalex.org/A5039419132"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5053,"has_fulltext":false,"cited_by_count":121,"citation_normalized_percentile":{"value":0.90378369,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"11","first_page":"1963","last_page":"1965"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.45249998569488525,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.45249998569488525,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.09399999678134918,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.04919999837875366,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8233228921890259},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7425112724304199},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.654578685760498},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.6143655180931091},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.586248517036438},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5761559009552002},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5218395590782166},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5215187668800354},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5063215494155884},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4188101887702942},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4184646010398865},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.41659706830978394},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.34768247604370117},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.27185118198394775},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20387759804725647},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14365339279174805}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8233228921890259},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7425112724304199},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.654578685760498},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.6143655180931091},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.586248517036438},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5761559009552002},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5218395590782166},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5215187668800354},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5063215494155884},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4188101887702942},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4184646010398865},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.41659706830978394},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.34768247604370117},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.27185118198394775},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20387759804725647},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14365339279174805},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","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":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty901","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty901","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1963/28759282/bty901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30358807","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30358807","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty901","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty901","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1963/28759282/bty901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5799999833106995}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1523894467","https://openalex.org/W2003347102","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2097146199","https://openalex.org/W2098466396","https://openalex.org/W2120902911","https://openalex.org/W2131026689","https://openalex.org/W2131271579","https://openalex.org/W2143842034","https://openalex.org/W2159954944","https://openalex.org/W2344352022","https://openalex.org/W2742651834","https://openalex.org/W2952488643"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W2046541848","https://openalex.org/W22571951","https://openalex.org/W4384009753","https://openalex.org/W2791776396","https://openalex.org/W4286531993","https://openalex.org/W2964820744","https://openalex.org/W4247858078"],"abstract_inverted_index":{"SUMMARY:":[0],"UGENE":[1,9,29,104,119],"is":[2,65,100,114,120],"a":[3,14,37,98],"free,":[4],"open-source,":[5],"cross-platform":[6],"bioinformatics":[7],"software.":[8],"deploys":[10],"pre-defined":[11],"pipelines":[12],"and":[13,21,50,97,127,129],"flexible":[15],"instrument":[16],"to":[17,90],"design":[18],"new":[19,28],"workflows":[20,82],"visually":[22],"build":[23],"multi-step":[24],"analytics":[25],"pipelines.":[26],"The":[27],"v.1.31":[30],"release":[31],"offers":[32],"graphical,":[33],"user-friendly":[34],"wrapping":[35],"of":[36,39,77],"number":[38],"popular":[40],"command-line":[41],"metagenomics":[42],"classification":[43,63],"programs":[44],"(Kraken,":[45],"CLARK,":[46],"DIAMOND),":[47],"combinable":[48],"serially":[49],"in":[51,74,125],"parallel":[52],"through":[53,67],"the":[54,68,75,95,103],"workflow":[55],"designer,":[56],"with":[57,71,94,108],"multiple,":[58],"customizable":[59],"reference":[60],"databases.":[61],"Ensemble":[62],"voting":[64],"available":[66,101,121],"WEVOTE":[69],"algorithm,":[70],"augmented":[72],"output":[73],"form":[76],"detailed":[78],"table":[79],"reports.":[80],"Pre-built":[81],"(which":[83],"include":[84],"all":[85],"steps":[86],"from":[87],"data":[88],"cleaning":[89],"summaries)":[91],"are":[92],"included":[93],"installation":[96],"tutorial":[99],"on":[102],"website.":[105],"Further":[106],"expansion":[107],"multiple":[109],"visualization":[110],"tools":[111],"for":[112],"reports":[113],"planned.":[115],"AVAILABILITY":[116],"AND":[117],"IMPLEMENTATION:":[118],"at":[122],"http://ugene.net/,":[123],"implemented":[124],"C++":[126],"Qt,":[128],"released":[130],"under":[131],"GNU":[132],"General":[133],"Public":[134],"License":[135],"(GPL)":[136],"version":[137],"2.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}