{"id":"https://openalex.org/W2133233871","doi":"https://doi.org/10.1093/bioinformatics/bts731","title":"NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets","display_name":"NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets","publication_year":2013,"publication_date":"2013-01-12","ids":{"openalex":"https://openalex.org/W2133233871","doi":"https://doi.org/10.1093/bioinformatics/bts731","mag":"2133233871","pmid":"https://pubmed.ncbi.nlm.nih.gov/23314324"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts731","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts731","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/494/48895499/bioinformatics_29_4_494.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/29/4/494/48895499/bioinformatics_29_4_494.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061355669","display_name":"Marcus R. Breese","orcid":"https://orcid.org/0000-0002-6870-0228"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcus R. Breese","raw_affiliation_strings":["1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100337366","display_name":"Yunlong Liu","orcid":"https://orcid.org/0000-0003-4650-3466"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yunlong Liu","raw_affiliation_strings":["1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100337366"],"corresponding_institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":6.0473,"has_fulltext":false,"cited_by_count":320,"citation_normalized_percentile":{"value":0.97312277,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"29","issue":"4","first_page":"494","last_page":"496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9860000014305115,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9724000096321106,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.8841469883918762},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8599465489387512},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7844749689102173},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7419627904891968},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6958850622177124},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.6271677017211914},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6045393943786621},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.591340959072113},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5342774391174316},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4402920603752136},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4025719165802002},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3736405670642853},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3501242399215698},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3394056558609009},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3305330276489258}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8841469883918762},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8599465489387512},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7844749689102173},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7419627904891968},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6958850622177124},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.6271677017211914},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6045393943786621},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.591340959072113},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5342774391174316},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4402920603752136},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4025719165802002},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3736405670642853},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3501242399215698},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3394056558609009},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3305330276489258},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts731","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts731","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/494/48895499/bioinformatics_29_4_494.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:23314324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23314324","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2907606","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3570212","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts731","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts731","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/494/48895499/bioinformatics_29_4_494.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":[],"awards":[{"id":"https://openalex.org/G1101252293","display_name":null,"funder_award_id":"U54 RR025761","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G1338581810","display_name":null,"funder_award_id":"U54 CA113001","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1555140389","display_name":null,"funder_award_id":"CA113001","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4681174381","display_name":null,"funder_award_id":"GM088076","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5316845550","display_name":null,"funder_award_id":"AA017941","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G583498415","display_name":null,"funder_award_id":"UL1-RR025761","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G6573407957","display_name":null,"funder_award_id":"R21 AA017941","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G724942601","display_name":null,"funder_award_id":"C06-RR020128","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G788200859","display_name":null,"funder_award_id":"R01GM088076","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G863822445","display_name":null,"funder_award_id":"C06 RR020128\u201001","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320309408","display_name":"Indiana Clinical and Translational Sciences Institute","ror":"https://ror.org/022t7q367"},{"id":"https://openalex.org/F4320337330","display_name":"National Institute on Alcohol Abuse and Alcoholism","ror":"https://ror.org/02jzrsm59"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2133233871.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1981194976","https://openalex.org/W1983070417","https://openalex.org/W2087064593","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2117608012","https://openalex.org/W2128016314","https://openalex.org/W2149992227","https://openalex.org/W2154431984"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W2546377002","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W4285209474","https://openalex.org/W2789551765","https://openalex.org/W3097598351"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"NGSUtils":[2,41],"is":[3,42],"a":[4,28,45],"suite":[5],"of":[6],"software":[7],"tools":[8,26],"for":[9,33],"manipulating":[10],"data":[11,34,80],"common":[12],"to":[13],"next-generation":[14],"sequencing":[15],"experiments,":[16],"such":[17],"as":[18],"FASTQ,":[19],"BED":[20],"and":[21,30,36,39,48,54,59,65],"BAM":[22],"format":[23],"files.":[24],"These":[25],"provide":[27],"stable":[29],"modular":[31],"platform":[32],"management":[35],"analysis.":[37],"Availability":[38],"implementation:":[40],"available":[43,82],"under":[44],"BSD":[46],"license":[47],"works":[49],"on":[50],"Mac":[51],"OS":[52],"X":[53],"Linux":[55],"systems.":[56],"Python":[57],"2.6+":[58],"virtualenv":[60],"are":[61,81],"required.":[62],"More":[63],"information":[64],"source":[66],"code":[67],"may":[68],"be":[69],"obtained":[70],"from":[71],"the":[72],"website:":[73],"http://ngsutils.org.":[74],"Contact:":[75],"yunliu@iupui.edu":[76],"Supplemental":[77],"information:":[78],"Supplementary":[79],"at":[83],"Bioinformatics":[84],"online.":[85]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":46},{"year":2019,"cited_by_count":34},{"year":2018,"cited_by_count":28},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
