MIDAS
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Description
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.
Required Modules
Serial
- gcc/5.2.0
- midas
System Variables
- HPC_{{#uppercase:midas}}_DIR - installation directory
Citation
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.]