TransFlow: a Snakemake workflow for transmission analysis ofMycobacterium tuberculosiswhole-genome sequencing data

Abstract

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. Availability TransFlow is free available at https://github.com/cvn001/transflow. Supplementary information Supplementary data are available at Bioinformatics online.