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Metagenomic Intra-Species Diversity Analysis 2

Metagenomic Intra-Species Diversity Analysis (MIDAS) is an integrated pipeline for profiling strain-level genomic variations in shotgun metagenomic data. The standard MIDAS workflow harnesses a reference database of 5,926 species extracted from 30,000 genomes (MIDAS DB v1.2).

MIDAS 2.0 used the same analysis workflow as the original MIDAS tool, and is engineered to work with more comprehensive MIDAS Reference Databases (MIDAS DBs), and to run on collections of thousands of samples in a fast and scalable manner. This page is focused specifically on the analysis steps, and for information about the MIDAS DB, including the target layout of MIDAS DB.