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.
- HPC_MIDAS_DIR - installation directory
If you publish research that uses midas you have to cite it as follows:
Nayfach, S. and Pollard, KS. "Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria". bioRxiv 2015.