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An integrated pipeline for estimating strain-level genomic variation from metagenomic data
Python Perl
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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
  1. Reference databse
  1. Run MIDAS on a single sample:
  1. Merge MIDAS results across samples:
  1. Example scripts for analyzing gene content and SNPs:
  1. Citing
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