License: This is an open access collection distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this collection and it's working
Created: July 28, 2022
Last Modified: July 29, 2022
Collection Integer ID: 67834
Keywords: genotyping, strain, microbiome, single nucleotide variant, copy number variant, metagenomic read, metagenomic read mapping filter, public microbial genome collection, end metagenomic read, reference database to the microbial community, raw sequencing reads to population, raw sequencing read, metagenotyping tool, sequencing library, microbial community, providing rich genetic data, metagenome, multiple bacterial species, gene copy number variant, level ecology of microbial community, rich genetic data, sequencing, genome, common use cases of midas2, detected variant, midas2, mixture of multiple bacterial species, comprehensive reference database, using comprehensive reference database, reference database, genetic analysis, hundreds of species, gene, mida
Abstract
The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants (CNVs) in metagenomes using comprehensive reference databases built from public microbial genome collections (“metagenotyping”). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. Here we present four basic protocols for the most common use cases of MIDAS2, along with two supporting protocols for installation and advanced use. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities.
