README.md

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

4. Run MIDAS on a single sample:

• Estimate species abundance
• Predict pan-genome gene content
• Call single nucleotide polymorphisms

5. Merge MIDAS results across samples:

• Merge species abundance
• Merge gene content
• Merge SNPs

6. Example scripts for analyzing gene content and SNPs:

• Core-genome phylogenetic trees
• Population diversity
• Strain tracking
• Gene content dynamics

7. Citing