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

Abstract

Summary: 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, and finally perform metagenotyping. For proof of concept, the protocol leverages public whole-genome sequences to metagenotype a synthetic community.For complete details on the use and execution of this protocol, please refer to Shi et al. (2022a)1 and Shi et al. (2022b).2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Sequence analysis
• Genetics
• Genomics
• Microbiology
• Evolutionary biology