metaSNV

metaSNV performs single nucleotide variant (SNV) detection and population-genetic analyses from metagenomic read alignments to reference genomes.

Key Features:

• Input Flexibility: Accepts nucleotide sequence alignments in standard SAM/BAM format as input.
• Comprehensive SNV Calling: Performs SNV calling at both individual-sample and dataset-wide levels.
• Statistical Analysis: Reports allele frequencies and nucleotide diversity for each species in the dataset.
• Comparative Metrics: Computes distance measures that enable comparison of genomic variation across metagenomic samples and tracking of strain-specific variants over time.
• Efficiency and Storage Optimization: Benchmarked against MIDAS, showing faster processing times and a reduced storage footprint without compromising result accuracy.

Scientific Applications:

• Microbial ecology: Enables SNV-based characterization of genetic diversity and population structure across thousands of bacterial and archaeal species.
• Evolutionary biology and population genetics: Supports analyses of allele frequency distributions, nucleotide diversity, genetic distances, and fixation indices within microbial communities.
• Longitudinal metagenomics and strain tracking: Facilitates detection and temporal tracking of strain-specific variants in environmental and host-associated microbiomes.

Methodology:

Uses nucleotide sequence alignments to reference genomes (SAM/BAM) for SNV calling and computes allele frequencies, nucleotide diversity, distance measures and fixation indices across samples.