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CholeraSeq is implemented in Nextflow with a modular design building upon the nf-core community standards.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf665","type":"journal-article","created":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T13:05:44Z","timestamp":1765458344000},"source":"Crossref","is-referenced-by-count":0,"title":["CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation"],"prefix":"10.1093","volume":"42","author":[{"given":"Massimiliano S","family":"Tagliamonte","sequence":"first","affiliation":[{"name":"Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, FL, 32601,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abhinav","family":"Sharma","sequence":"additional","affiliation":[{"name":"DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, 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