{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T15:15:36Z","timestamp":1777043736967,"version":"3.51.4"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"name":"Cooperative Agreement","award":["NU60OE000104"],"award-info":[{"award-number":["NU60OE000104"]}]},{"name":"Centers for Disease Control and Prevention through the Association of Public Health Laboratories"},{"name":"TaxTriage"},{"DOI":"10.13039\/100000061","name":"NIH Fogarty International Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000061","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NAVSEA IDIQ","award":["N00024-22-D-6404"],"award-info":[{"award-number":["N00024-22-D-6404"]}]},{"DOI":"10.13039\/100000016","name":"Department of Health and Human Services","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008482","name":"Association of Public Health Laboratories","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008482","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow\u2122 (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code for TaxTriage is freely available at https:\/\/github.com\/jhuapl-bio\/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https:\/\/zenodo.org\/records\/17081354 to permit reproducible analysis as described in this manuscript.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag119","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T11:38:49Z","timestamp":1774957129000},"source":"Crossref","is-referenced-by-count":0,"title":["TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection"],"prefix":"10.1093","volume":"42","author":[{"given":"Brian","family":"Merritt","sequence":"first","affiliation":[{"name":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6522-138X","authenticated-orcid":false,"given":"Jeremy D","family":"Ratcliff","sequence":"additional","affiliation":[{"name":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stanley","family":"Ta","sequence":"additional","affiliation":[{"name":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gunars","family":"Osis","sequence":"additional","affiliation":[{"name":"ASRT Inc., Contractor for Office of Laboratory Systems and Response, Centers for Disease Control and Prevention , Smyrna, GA 30080,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew R","family":"Mauldin","sequence":"additional","affiliation":[{"name":"Office of Readiness and Response, Centers for Disease Control and Prevention , Atlanta, GA 30333,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1807-2785","authenticated-orcid":false,"given":"Peter M","family":"Thielen","sequence":"additional","affiliation":[{"name":"Johns Hopkins Applied Physics Laboratory , Laurel, MD 20723,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,4,1]]},"reference":[{"key":"2026042409465259900_btag119-B1","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1056\/NEJMsr1813907","article-title":"Pathogen genomics in public health","volume":"381","author":"Armstrong","year":"2019","journal-title":"N Engl J Med"},{"key":"2026042409465259900_btag119-B2","doi-asserted-by":"crossref","first-page":"001269","DOI":"10.1099\/mic.0.001269","article-title":"A comprehensive list of bacterial pathogens infecting humans","volume":"168","author":"Bartlett","year":"2022","journal-title":"Microbiology (Reading)"},{"key":"2026042409465259900_btag119-B3","doi-asserted-by":"publisher","first-page":"3522","DOI":"10.1038\/s41591-024-03275-1","article-title":"Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of Central nervous system infections","volume":"30","author":"Benoit","year":"2024","journal-title":"Nat Med"},{"key":"2026042409465259900_btag119-B16322740","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2026042409465259900_btag119-B4","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00466-19","article-title":"Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing data sets","volume":"57","author":"Brinkmann","year":"2019","journal-title":"J Clin Microbiol"},{"key":"2026042409465259900_btag119-B5","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/s13073-024-01380-x","article-title":"Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses. 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