MIDAS

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Description

midas website  

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.

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