Welcome to MIDAS2

Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is an integrated pipeline for profiling single nucleotide variants (SNVs) and gene copy number variants (CNVs) in shotgun metagenomic reads. MIDAS2 implements the same analyses as the original MIDAS, but re-engineered to addresses the computational challenges presented by increasingly large reference genome databases.

MIDAS2 was developed by Chunyu Zhao and Boris Dimitrov in the Pollard Lab at Chan Zuckerberg Biohub. MIDAS2 expands on the original MIDAS developed by Stephen Nayfach.

For MIDAS2, we have already built two MIDASDBs from large, public, microbial genome databases: UHGG 1.0 and GTDB r202.

Source code is available on GitHub.

Publication is available in Bioinformatics.

Contents

• Quickstart
• Installation
• MIDAS2 Overview
• Module: Species Selection
• Module: Single Nucleotide Variant Analysis
• Module: Copy Number Variant Analysis
• Downloading the MIDASDB
• Output Files and Directory Layout
• Advanced Topics
• Example Questions
• What percent of observed data can be accounted for by the major and minor alleles?
• What is the detection power of MIDAS2 when multiple strains are present per species?
• Glossary
• Acknowledgements