SNPTB: nucleotide variant identification and annotation in Mycobacterium tuberculosis genomes

Summary Whole genome sequencing (WGS) has become a mainstay in biomedical research. The continually decreasing cost of sequencing has resulted in a data deluge that underlines the need for easy-to-use bioinformatics pipelines that can mine meaningful information from WGS data. SNPTB is one such pipeline that analyzes WGS data originating from in vitro or clinical samples of Mycobacterium tuberculosis and outputs high-confidence single nucleotide polymorphisms in the bacterial genome. The name of the mutated gene and the functional consequence of the mutation on the gene product is also determined. SNPTB utilizes open source software for WGS data analyses and is written primarily for biologists with minimal computational skills. Availability and implementation SNPTB is a python package and is available from https://github.com/aditi9783/SNPTB Contact [email protected] Supplementary information Tutorial for SNPTB is available at https://github.com/aditi9783/SNPTB/blob/master/docs/SNPTB_tutorial.md