Metagenomic Intra-Species Diversity Analysis System (MIDAS)

MIDAS is an integrated pipeline that leverages >30,000 reference genomes to estimate bacterial species abundance and strain-level genomic variation, including gene content and SNPs, from shotgun metagnomes.

Table of Contents

1. Getting started
   • How it works
   • Install or update software
   • Step-by-step tutorial
   • Docker-image
2. Reference databse
   • Download default database
   • Build your own custom database
3. Run MIDAS on a single sample:
   • Estimate species abundance
   • Predict pan-genome gene content
   • Call single nucleotide polymorphisms
4. Merge MIDAS results across samples:
   • Merge species abundance
   • Merge gene content
   • Merge SNPs
5. Example scripts for analyzing gene content and SNPs:
   • Core-genome phylogenetic trees
   • Population diversity
   • Strain tracking
   • Gene content dynamics
6. Citing