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and read mapping to metagenomically assembled genomes to detect potential etiological agents found in common across outbreak specimens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/uel3\/nf-UnO.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf436","type":"journal-article","created":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T16:08:18Z","timestamp":1754064498000},"source":"Crossref","is-referenced-by-count":1,"title":["nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9318-2694","authenticated-orcid":false,"given":"Candace","family":"Guzman-Cole","sequence":"first","affiliation":[{"name":"Enteric Diseases Laboratory Branch, Centers for Disease Control , Atlanta, GA 30322,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7972-1454","authenticated-orcid":false,"given":"Andrew D","family":"Huang","sequence":"additional","affiliation":[{"name":"Enteric Diseases Laboratory Branch, Centers for Disease Control , Atlanta, GA 30322,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,1]]},"reference":[{"key":"2025081905562767200_btaf436-B1","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2021","journal-title":"Nat Biotechnol"},{"year":"2010","author":"Andrews","key":"2025081905562767200_btaf436-B2"},{"key":"2025081905562767200_btaf436-B3","doi-asserted-by":"crossref","first-page":"1186424","DOI":"10.3389\/fmicb.2023.1186424","article-title":"Clinical metagenomics\u2014challenges and future 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