MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline.

ABSTRACT: The MTBseq pipeline, published in 2018, was designed to address bioinformatics challenges in tuberculosis (TB) research using whole-genome sequencing (WGS) data. It was the first publicly available tool on GitHub to perform full analysis of WGS data for Mycobacterium tuberculosis complex (MTBC) encompassing quality control through mapping, variant calling for lineage classification, drug resistance prediction, and phylogenetic inference. However, the pipeline's architecture is not optimal for analyses on high-performance computing or cloud computing environments that often involve large datasets. To overcome this limitation, we developed MTBseq-nf, a Nextflow wrapper that provides parallelization for faster execution speeds in addition to several other significant enhancements. The

SUBMITTER: Sharma A 

PROVIDER: S-EPMC12734750 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature