MutVis

MutVis analyzes mutational patterns from whole genome sequencing data to extract and visualize base-pair substitution spectra and mutational signatures for bacterial genomics research.

Key Features:

• Automated Workflow: Uses Snakemake to orchestrate Python and R scripts and integrate publicly available bioinformatics tools.
• Variant Calling and Processing: Supports variant calling from whole genome sequencing and processes Variant Call Format (VCF) files to extract mutation information.
• Transition and Transversion Analysis: Provides analyses of transitions (Ti) and transversions (Tv) with a 6-base substitution classification at both genome and gene levels.
• Base Pair Substitution Spectrum (BPS): Produces 96-profile BPS plots for high-resolution visualization of base-pair substitutions.
• Mutational Count Matrix: Generates mutational count matrices to quantify and organize mutation data.
• Mutation Signature Extraction: Applies non-negative matrix factorization (NMF) to derive signatures from BPS and presents relative contributions via hierarchically clustered heatmaps.

Scientific Applications:

• Bacterial Mutational Signature Characterization: Characterizes mutational signatures across bacterial species or within specific genomes to study evolutionary processes and adaptive mechanisms.
• Mycobacterium tuberculosis Surveillance: Applied to geographically diverse Mycobacterium tuberculosis strains from the PATRIC TB-ARC Antibiotic Resistance Catalog (n = 963) to analyze mutation biases and characteristic mutational signatures.

Methodology:

An automated Snakemake workflow runs Python and R scripts to perform variant calling from whole genome sequencing, process VCF files, build mutational count matrices, extract signatures using non-negative matrix factorization (NMF) with hierarchical clustering for heatmaps, and visualize results via Ti/Tv plots and 96-profile BPS plots.