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.
Environment Modules
Run module spider midas to find out what environment modules are available for this application.
System Variables
- HPC_MIDAS_DIR - installation directory
- HPC_MIDAS_BIN - executable directory
- MIDAS_DB - reference database directory
Citation
If you publish research that uses midas you have to cite it as follows:
S Nayfach, B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria". Genome Research 2016. doi:10.1101/gr.201863.115