{"id":"https://openalex.org/W2390359191","doi":"https://doi.org/10.1371/journal.pcbi.1004658","title":"NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes","display_name":"NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes","publication_year":2016,"publication_date":"2016-01-28","ids":{"openalex":"https://openalex.org/W2390359191","doi":"https://doi.org/10.1371/journal.pcbi.1004658","mag":"2390359191","pmid":"https://pubmed.ncbi.nlm.nih.gov/26820746"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004658","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004658","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004658&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004658&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058766687","display_name":"Gabriel A. Al\u2010Ghalith","orcid":"https://orcid.org/0000-0002-6953-6319"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel A. Al-Ghalith","raw_affiliation_strings":["Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, United States of America","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073653250","display_name":"Emmanuel Montassier","orcid":"https://orcid.org/0000-0002-2313-1172"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Emmanuel Montassier","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America","University of Nantes, Nantes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"University of Nantes, Nantes, France","institution_ids":["https://openalex.org/I97188460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058516038","display_name":"Henry N. Ward","orcid":"https://orcid.org/0000-0002-9869-9790"},"institutions":[{"id":"https://openalex.org/I153592363","display_name":"Lawrence University","ror":"https://ror.org/005w9jb47","country_code":"US","type":"education","lineage":["https://openalex.org/I153592363"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henry N. Ward","raw_affiliation_strings":["Lawrence University, Appleton, Wisconsin, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence University, Appleton, Wisconsin, United States of America","institution_ids":["https://openalex.org/I153592363"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082358375","display_name":"Dan Knights","orcid":"https://orcid.org/0000-0002-8205-2511"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dan Knights","raw_affiliation_strings":["Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, United States of America","Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, United States of America","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082358375"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.9197,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.96610377,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"12","issue":"1","first_page":"e1004658","last_page":"e1004658"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9882000088691711,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6790367364883423},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6331850290298462},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5822029709815979},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5787150859832764},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.5313552021980286},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44215187430381775},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3638422191143036},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.34998542070388794},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.325336754322052},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3159014582633972},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.281235933303833},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.2117956578731537},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16938289999961853}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6790367364883423},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6331850290298462},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5822029709815979},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5787150859832764},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.5313552021980286},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44215187430381775},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3638422191143036},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34998542070388794},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.325336754322052},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3159014582633972},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.281235933303833},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.2117956578731537},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16938289999961853},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","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":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1004658","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004658","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004658&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26820746","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26820746","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:d276b358482a4dd39a36a68c353e31e0","is_oa":true,"landing_page_url":"https://doaj.org/article/d276b358482a4dd39a36a68c353e31e0","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":"PLoS Computational Biology, Vol 12, Iss 1, p e1004658 (2016)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/2630170","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/NINJA_OPS_Fast_Accurate_Marker_Gene_Alignment_Using_Concatenated_Ribosomes/2630170","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4731464","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4731464","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004658","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004658","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004658&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3361901465","display_name":null,"funder_award_id":"R01AI121383","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G553188523","display_name":null,"funder_award_id":"R01 AI121383","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6517130499","display_name":null,"funder_award_id":"R01AI121383","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6691802863","display_name":null,"funder_award_id":"UL1 TR000114","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"}],"funders":[{"id":"https://openalex.org/F4320325352","display_name":"Soci\u00e9t\u00e9 Nationale Fran\u00e7aise de Gastro-Ent\u00e9rologie","ror":"https://ror.org/04c6sc363"},{"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"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1039840915","https://openalex.org/W1513515886","https://openalex.org/W1975904117","https://openalex.org/W2000484009","https://openalex.org/W2014650117","https://openalex.org/W2020281045","https://openalex.org/W2030782070","https://openalex.org/W2072970694","https://openalex.org/W2085284704","https://openalex.org/W2097341408","https://openalex.org/W2100955902","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2108718991","https://openalex.org/W2110375946","https://openalex.org/W2114225677","https://openalex.org/W2124351063","https://openalex.org/W2124799197","https://openalex.org/W2124927293","https://openalex.org/W2126218947","https://openalex.org/W2128769815","https://openalex.org/W2137177315","https://openalex.org/W2148364066","https://openalex.org/W2149021569","https://openalex.org/W2156125289","https://openalex.org/W2156619206","https://openalex.org/W2170551349","https://openalex.org/W6650339521"],"related_works":["https://openalex.org/W4283384467","https://openalex.org/W4210830088","https://openalex.org/W2909852840","https://openalex.org/W4225379983","https://openalex.org/W2794975275","https://openalex.org/W2110353968","https://openalex.org/W54719527","https://openalex.org/W3047096471","https://openalex.org/W2020006618","https://openalex.org/W2564898509"],"abstract_inverted_index":{"The":[0],"explosion":[1],"of":[2,8,18,24,35,108,119,185,194,221],"bioinformatics":[3],"technologies":[4],"in":[5,21,227],"the":[6,22,109,123,126,195],"form":[7,23],"next":[9,36],"generation":[10,37],"sequencing":[11,38,63],"(NGS)":[12],"has":[13],"facilitated":[14],"a":[15,32,87,192,200,205,211,232],"massive":[16],"influx":[17],"genomics":[19],"data":[20],"short":[25,44],"reads.":[26],"Short":[27],"read":[28],"mapping":[29],"is":[30,142,199],"therefore":[31],"fundamental":[33],"component":[34],"pipelines":[39],"which":[40,65],"routinely":[41],"match":[42],"these":[43],"reads":[45,136],"against":[46],"reference":[47,116,121],"genomes":[48],"for":[49,85,134,216],"contig":[50],"assembly.":[51],"However,":[52],"such":[53],"techniques":[54],"have":[55,66],"seldom":[56],"been":[57],"applied":[58,163],"to":[59,165,173],"microbial":[60],"marker":[61,96],"gene":[62,97],"studies,":[64,169],"mostly":[67],"relied":[68],"on":[69,231],"novel":[70,92],"heuristic":[71],"approaches.":[72],"We":[73,162],"propose":[74],"NINJA":[75,84,105,141,164,198],"Is":[76],"Not":[77],"Just":[78],"Another":[79],"OTU-Picking":[80],"Solution":[81],"(NINJA-OPS,":[82],"or":[83,103,174,187],"short),":[86],"fast":[88],"and":[89,145,148,190,209],"highly":[90],"accurate":[91],"method":[93],"enabling":[94],"reference-based":[95,178],"matching":[98],"(picking":[99],"Operational":[100],"Taxonomic":[101],"Units,":[102],"OTUs).":[104],"takes":[106,204],"advantage":[107],"Burrows-Wheeler":[110],"(BW)":[111],"alignment":[112],"using":[113,191],"an":[114,183,217],"artificial":[115],"chromosome":[117],"composed":[118],"concatenated":[120],"sequences,":[122],"\"concatesome,\"":[124],"as":[125],"BW":[127],"input.":[128],"Other":[129],"features":[130],"include":[131],"automatic":[132],"support":[133],"paired-end":[135],"with":[137,159],"arbitrary":[138],"insert":[139],"sizes.":[140],"also":[143],"free":[144],"open":[146],"source":[147],"implements":[149],"several":[150,166],"pre-filtering":[151],"methods":[152,180],"that":[153,203],"elicit":[154],"substantial":[155],"speedup":[156,189],"when":[157],"coupled":[158],"existing":[160],"tools.":[161],"published":[167],"microbiome":[168,224],"obtaining":[170],"accuracy":[171],"similar":[172],"better":[175],"than":[176],"previous":[177],"OTU-picking":[179],"while":[181],"achieving":[182],"order":[184],"magnitude":[186],"more":[188],"fraction":[193],"memory":[196],"footprint.":[197],"complete":[201],"pipeline":[202],"FASTA-formatted":[206],"input":[207],"file":[208,215],"outputs":[210],"QIIME-formatted":[212],"taxonomy-annotated":[213],"BIOM":[214],"entire":[218],"MiSeq":[219],"run":[220],"human":[222],"gut":[223],"16S":[225],"genes":[226],"under":[228],"10":[229],"minutes":[230],"dual-core":[233],"laptop.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}