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DOE OSTI · 2234195

Maast: genotyping thousands of microbial strains efficiently

Shi, Zhou Jason·Nayfach, Stephen·Pollard, Katherine S.
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Abstract

Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatics tool, Maast, which empowers population genetic meta-analysis of microbes at an unrivaled scale. Maast implements a novel algorithm to heuristically identify a minimal set of diverse conspecific genomes, then constructs a reliable SNP panel for each species, and enables rapid and accurate genotyping using a hybrid of whole-genome alignment and k-mer exact matching. We demonstrate Maast’s utility by genotyping thousands of Helicobacter pylori strains and tracking SARS-CoV-2 diversification.

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Shi, Zhou Jason, Nayfach, Stephen, Pollard, Katherine S.. 2023-08-10. Maast: genotyping thousands of microbial strains efficiently. https://doi.org/10.1186/s13059-023-03030-8

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