Genome analysis TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data

被引：4
作者：
Pan, Junhang [1 ]
Li, Xiangchen [2 ]
Zhang, Mingwu [1 ]
Lu, Yewei [2 ]
Zhu, Yelei [1 ]
Wu, Kunyang [1 ]
Wu, Yiwen [3 ]
Wang, Weixin [2 ]
Chen, Bin [1 ]
Liu, Zhengwei [1 ]
Wang, Xiaomeng [1 ]
Gao, Junshun [2 ]
机构：
[1] Zhejiang Prov Ctr Dis Control & Prevent, Inst TB Control, Hangzhou 310051, Zhejiang, Peoples R China
[2] Key Lab Precis Med Diag & Monitoring Res Zhejiang, Hangzhou 310020, Zhejiang, Peoples R China
[3] Zhejiang Chinese Med Univ, Dept Med Oncol, Hangzhou 310053, Zhejiang, Peoples R China
来源：
BIOINFORMATICS | 2023年 / 39卷 / 01期
关键词：
SURVEILLANCE; OUTBREAKS;
D O I：
10.1093/bioinformatics/btac785
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Motivation: 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. Results: 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.
引用
收藏
页数：7
相关论文
共 49 条
  • [1] Anaconda,Inc, 2020, AN SOFTW DISTR COMP
  • [2] Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population
    Ayabina, Diepreye
    Ronning, Janne O.
    Alfsnes, Kristian
    Debech, Nadia
    Brynikisrud, Ola B.
    Arnesen, Trude
    Norheim, Gunnstein
    Mengshoel, Anne-Torunn
    Rykkvin, Rikard
    Dahle, Ulf R.
    Colijn, Caroline
    Eldholm, Vegard
    [J]. MICROBIAL GENOMICS, 2018, 4 (10):
  • [3] Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses
    Bainomugisa, Arnold
    Meumann, Ella M.
    Rajahram, Giri Shan
    Ong, Rick Twee-Hee
    Coin, Lachlan
    Paul, Dawn Carmel
    William, Timothy
    Coulter, Christopher
    Ralph, Anna P.
    [J]. MICROBIAL GENOMICS, 2021, 7 (05):
  • [4] Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland
    Bjorn-Mortensen, K.
    Soborg, B.
    Koch, A.
    Ladefoged, K.
    Merker, M.
    Lillebaek, T.
    Andersen, A. B.
    Niemann, S.
    Kohl, T. A.
    [J]. SCIENTIFIC REPORTS, 2016, 6
  • [5] Trimmomatic: a flexible trimmer for Illumina sequence data
    Bolger, Anthony M.
    Lohse, Marc
    Usadel, Bjoern
    [J]. BIOINFORMATICS, 2014, 30 (15) : 2114 - 2120
  • [6] Borrell S, 2009, INT J TUBERC LUNG D, V13, P1456
  • [7] outbreaker2: a modular platform for outbreak reconstruction
    Campbell, Finlay
    Didelot, Xavier
    Fitzjohn, Rich
    Ferguson, Neil
    Cori, Anne
    Jombart, Thibaut
    [J]. BMC BIOINFORMATICS, 2018, 19
  • [8] Molecular surveillance of multi- and extensively drug-resistant tuberculosis transmission in the European Union from 2003 to 2011
    De Beer, J. L.
    Kodmon, C.
    van der Werf, M. J.
    van Ingen, J.
    van Soolingen, D.
    [J]. EUROSURVEILLANCE, 2014, 19 (11): : 5 - 13
  • [9] Drug Susceptibility of Mycobacterium tuberculosis Beijing Genotype and Association with MDR TB
    de Steenwinkel, Jurriaan E. M.
    ten Kate, Marian T.
    de Knegt, Gerjo J.
    Kremer, Kristin
    Aarnoutse, Rob E.
    Boeree, Martin J.
    Verbrugh, Henri A.
    van Soolingen, Dick
    Bakker-Woudenberg, Irma A. J. M.
    [J]. EMERGING INFECTIOUS DISEASES, 2012, 18 (04) : 660 - 663
  • [10] A framework for variation discovery and genotyping using next-generation DNA sequencing data
    DePristo, Mark A.
    Banks, Eric
    Poplin, Ryan
    Garimella, Kiran V.
    Maguire, Jared R.
    Hartl, Christopher
    Philippakis, Anthony A.
    del Angel, Guillermo
    Rivas, Manuel A.
    Hanna, Matt
    McKenna, Aaron
    Fennell, Tim J.
    Kernytsky, Andrew M.
    Sivachenko, Andrey Y.
    Cibulskis, Kristian
    Gabriel, Stacey B.
    Altshuler, David
    Daly, Mark J.
    [J]. NATURE GENETICS, 2011, 43 (05) : 491 - +
12345