{"id":"https://openalex.org/W7148588278","doi":"https://doi.org/10.1093/bioinformatics/btag119","title":"TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection","display_name":"TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection","publication_year":2026,"publication_date":"2026-03-31","ids":{"openalex":"https://openalex.org/W7148588278","doi":"https://doi.org/10.1093/bioinformatics/btag119","pmid":"https://pubmed.ncbi.nlm.nih.gov/41923365"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag119","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag119","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064810387","display_name":"Brian Merritt","orcid":null},"institutions":[{"id":"https://openalex.org/I2802946424","display_name":"Johns Hopkins University Applied Physics Laboratory","ror":"https://ror.org/029pp9z10","country_code":"US","type":"facility","lineage":["https://openalex.org/I145311948","https://openalex.org/I2802946424"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Merritt","raw_affiliation_strings":["Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","institution_ids":["https://openalex.org/I2802946424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072119815","display_name":"Jeremy Ratcliff","orcid":"https://orcid.org/0000-0001-6522-138X"},"institutions":[{"id":"https://openalex.org/I2802946424","display_name":"Johns Hopkins University Applied Physics Laboratory","ror":"https://ror.org/029pp9z10","country_code":"US","type":"facility","lineage":["https://openalex.org/I145311948","https://openalex.org/I2802946424"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy D Ratcliff","raw_affiliation_strings":["Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,"],"raw_orcid":"https://orcid.org/0000-0001-6522-138X","affiliations":[{"raw_affiliation_string":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","institution_ids":["https://openalex.org/I2802946424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120221293","display_name":"Stanley Ta","orcid":"https://orcid.org/0000-0002-1816-2257"},"institutions":[{"id":"https://openalex.org/I2802946424","display_name":"Johns Hopkins University Applied Physics Laboratory","ror":"https://ror.org/029pp9z10","country_code":"US","type":"facility","lineage":["https://openalex.org/I145311948","https://openalex.org/I2802946424"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stanley Ta","raw_affiliation_strings":["Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","institution_ids":["https://openalex.org/I2802946424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061035446","display_name":"Gunars Osis","orcid":"https://orcid.org/0000-0002-0613-737X"},"institutions":[{"id":"https://openalex.org/I4210102376","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/00qzjvm58","country_code":"UG","type":"government","lineage":["https://openalex.org/I4210102376"]}],"countries":["UG"],"is_corresponding":false,"raw_author_name":"Gunars Osis","raw_affiliation_strings":["ASRT Inc., Contractor for Office of Laboratory Systems and Response, Centers for Disease Control and Prevention , Smyrna, GA 30080,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ASRT Inc., Contractor for Office of Laboratory Systems and Response, Centers for Disease Control and Prevention , Smyrna, GA 30080,","institution_ids":["https://openalex.org/I4210102376"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055949063","display_name":"Matthew R. Mauldin","orcid":"https://orcid.org/0000-0002-3807-2339"},"institutions":[{"id":"https://openalex.org/I4210096256","display_name":"Office of Readiness and Response","ror":"https://ror.org/00sdb8f83","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210096256"]},{"id":"https://openalex.org/I4210102376","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/00qzjvm58","country_code":"UG","type":"government","lineage":["https://openalex.org/I4210102376"]}],"countries":["UG","US"],"is_corresponding":false,"raw_author_name":"Matthew R Mauldin","raw_affiliation_strings":["Office of Readiness and Response, Centers for Disease Control and Prevention , Atlanta, GA 30333,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Readiness and Response, Centers for Disease Control and Prevention , Atlanta, GA 30333,","institution_ids":["https://openalex.org/I4210102376","https://openalex.org/I4210096256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028027107","display_name":"Peter Thielen","orcid":"https://orcid.org/0000-0003-1807-2785"},"institutions":[{"id":"https://openalex.org/I2802946424","display_name":"Johns Hopkins University Applied Physics Laboratory","ror":"https://ror.org/029pp9z10","country_code":"US","type":"facility","lineage":["https://openalex.org/I145311948","https://openalex.org/I2802946424"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter M Thielen","raw_affiliation_strings":["Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,"],"raw_orcid":"https://orcid.org/0000-0003-1807-2785","affiliations":[{"raw_affiliation_string":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","institution_ids":["https://openalex.org/I2802946424"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.42585545,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6973999738693237,"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":0.6973999738693237,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.035100001841783524,"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/T10066","display_name":"Gut microbiota and health","score":0.01549999974668026,"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/metagenomics","display_name":"Metagenomics","score":0.8267999887466431},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7791000008583069},{"id":"https://openalex.org/keywords/pathogen","display_name":"Pathogen","score":0.4553999900817871},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4066999852657318},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.35179999470710754},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.32679998874664307}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8267999887466431},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7791000008583069},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6262999773025513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5235999822616577},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4578000009059906},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.4553999900817871},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4066999852657318},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3977999985218048},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.35179999470710754},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.32679998874664307},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2773999869823456},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.27730000019073486},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.2694999873638153},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.26429998874664307},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2542000114917755}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btag119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag119","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41923365","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41923365","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/btag119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag119","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320310555","display_name":"Association of Public Health Laboratories","ror":"https://ror.org/04d0f7957"},{"id":"https://openalex.org/F4320337356","display_name":"Fogarty International Center","ror":"https://ror.org/02xey9a22"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1954100204","https://openalex.org/W1975375203","https://openalex.org/W2045204781","https://openalex.org/W2061525000","https://openalex.org/W2085926377","https://openalex.org/W2094212509","https://openalex.org/W2103685216","https://openalex.org/W2108234281","https://openalex.org/W2113679889","https://openalex.org/W2123550299","https://openalex.org/W2137662380","https://openalex.org/W2170551349","https://openalex.org/W2171571559","https://openalex.org/W2432815617","https://openalex.org/W2561512876","https://openalex.org/W2587565773","https://openalex.org/W2605897695","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2884944393","https://openalex.org/W2913450144","https://openalex.org/W2914084957","https://openalex.org/W2948821061","https://openalex.org/W2951912016","https://openalex.org/W2990618091","https://openalex.org/W2997069256","https://openalex.org/W3001897055","https://openalex.org/W3099584446","https://openalex.org/W3131055609","https://openalex.org/W3135191472","https://openalex.org/W3157212212","https://openalex.org/W3170143789","https://openalex.org/W4211037082","https://openalex.org/W4223460124","https://openalex.org/W4225258284","https://openalex.org/W4283360071","https://openalex.org/W4297498241","https://openalex.org/W4310923015","https://openalex.org/W4376256177","https://openalex.org/W4389229252","https://openalex.org/W4392882513","https://openalex.org/W4393952367","https://openalex.org/W4396817679","https://openalex.org/W4396894261","https://openalex.org/W4402348265","https://openalex.org/W4404252573","https://openalex.org/W4404811976"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"TaxTriage":[1,157,163],"is":[2,158],"a":[3,65,94],"comprehensive":[4],"pathogen":[5,118],"identification":[6],"workflow":[7],"designed":[8],"for":[9,116,146,156],"both":[10,130],"short-":[11],"and":[12,16,24,38,61,90,105,119,125,133],"long-read":[13],"untargeted":[14],"DNA":[15],"RNA":[17],"sequencing":[18],"data.":[19,44],"Combining":[20],"read":[21],"classification,":[22],"mapping,":[23],"de":[25],"novo":[26],"assembly":[27],"approaches,":[28],"putative":[29],"pathogens":[30,37,89],"are":[31,48,79],"identified":[32,108],"through":[33],"comparisons":[34],"to":[35,111,142,172],"curated":[36],"abundance":[39],"expectations":[40],"from":[41],"healthy":[42],"cohort":[43],"Flexible":[45],"installation":[46,63],"options":[47,138],"enabled":[49],"using":[50],"Nextflow\u2122":[51],"(NF),":[52],"including":[53,69,93],"cloud":[54],"deployment":[55],"via":[56],"NF":[57],"Tower":[58],"(Seqera":[59],"Platform)":[60],"local":[62],"on":[64,168],"variety":[66],"of":[67,100,149],"systems,":[68],"standalone":[70],"installations":[71],"without":[72],"external":[73],"internet":[74],"access.":[75],"Final":[76],"analysis":[77,175],"summaries":[78],"compiled":[80],"into":[81],"an":[82],"Organism":[83],"Discovery":[84],"Report,":[85],"which":[86],"lists":[87],"likely":[88],"supporting":[91],"data,":[92],"custom":[95],"confidence":[96],"score.":[97],"RESULTS:":[98],"Evaluation":[99],"published":[101],"in":[102,178],"silico,":[103],"clinical,":[104],"outbreak":[106],"datasets":[107],"performance":[109,145],"comparable":[110],"alternative":[112],"cloud-based":[113],"processing":[114],"pipelines":[115],"expected":[117],"co-infection":[120],"detection":[121],"with":[122],"similar":[123],"sensitivity":[124],"increased":[126],"specificity.":[127],"To":[128],"support":[129],"public":[131],"health":[132],"veterinary":[134],"diagnostics":[135],"communities,":[136],"customization":[137],"have":[139],"been":[140,166],"incorporated":[141],"enable":[143],"improved":[144],"host":[147],"species":[148],"interest.":[150],"AVAILABILITY":[151],"AND":[152],"IMPLEMENTATION:":[153],"Source":[154],"code":[155],"freely":[159],"available":[160],"at":[161,170],"https://github.com/jhuapl-bio/taxtriage.":[162],"v2.1.1":[164],"has":[165],"archived":[167],"Zenodo":[169],"https://zenodo.org/records/17081354":[171],"permit":[173],"reproducible":[174],"as":[176],"described":[177],"this":[179],"manuscript.":[180]},"counts_by_year":[],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2026-04-03T00:00:00"}