{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,7]],"date-time":"2025-12-07T21:42:13Z","timestamp":1765143733430,"version":"3.41.2"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,5]],"date-time":"2022-12-05T00:00:00Z","timestamp":1670198400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National and Zhejiang Health Commission Scientific Research Fund","award":["WKJ-ZJ-2118"],"award-info":[{"award-number":["WKJ-ZJ-2118"]}]},{"name":"Medical Scientific Research Foundation of Zhejiang","award":["2019KY354"],"award-info":[{"award-number":["2019KY354"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Whole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>TransFlow is free available at https:\/\/github.com\/cvn001\/transflow.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac785","type":"journal-article","created":{"date-parts":[[2022,12,5]],"date-time":"2022-12-05T20:07:12Z","timestamp":1670270832000},"source":"Crossref","is-referenced-by-count":7,"title":["TransFlow: a Snakemake workflow for transmission analysis of<i>Mycobacterium tuberculosis<\/i>whole-genome sequencing data"],"prefix":"10.1093","volume":"39","author":[{"given":"Junhang","family":"Pan","sequence":"first","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangchen","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingwu","family":"Zhang","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yewei","family":"Lu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yelei","family":"Zhu","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kunyang","family":"Wu","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwen","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, Zhejiang Chinese Medical University , Hangzhou, Zhejiang 310053, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weixin","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Chen","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhengwei","family":"Liu","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaomeng","family":"Wang","sequence":"additional","affiliation":[{"name":"The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, Zhejiang 310051, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9040-2289","authenticated-orcid":false,"given":"Junshun","family":"Gao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Hangzhou, Zhejiang 310020, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,5]]},"reference":[{"year":"2020","author":"Anaconda,Inc","key":"2023010805380250900_btac785-B1"},{"key":"2023010805380250900_btac785-B2","first-page":"10","article-title":"Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population","volume":"4","author":"Ayabina","year":"2018","journal-title":"Microb. 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