MetaQuad: shared informative variants discovery in metagenomic samples.

ABSTRACT:

Motivation

Strain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge.

Results

MetaQuad utilizes a density-based clustering technique to effectively distinguish between shared variants and non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significant

SUBMITTER: Xu S 

PROVIDER: S-EPMC10932609 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature