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Article

Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.

STAR protocols - 17 Mar 2023

Shi Zhou Jason, Nayfach Stephen, Pollard Katherine S

Abstract excerpt

Genotyping single-nucleotide polymorphisms (SNPs) in microbiomes enables strain-level quantification. In this protocol, we describe a computational pipeline that performs fast and accurate SNP genotyping using metagenomic data. We first demonstrate how to use Maast to catalog SNPs from microbial genomes. Then we use GT-Pro to extract unique SNP-covering k-mers, optimize a data structure for storing these k-mers,...

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Identifiers

PMID: 36856771
DOI: 10.1016/j.xpro.2022.101964
PMCID: PMC10037184

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