1.3.2

Metagenomic Intra-Species Diversity Analysis System (MIDAS) container

Main tool: MIDAS

Additional tools:

• samtools v1.4
• bowtie2 v2.4.4
• hmmer v3.3.2
• vsearch v2.21.1

Full documentation: https://github.com/snayfach/MIDAS

Note

This docker image does not contain reference database. Users should download the default database or create their own.

Default database found here: http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.2.tar.gz

Example usage

run_midas.py species /path/to/outdir -1 /path/to/reads_1.fq.gz -2 /path/to/reads_2.fq.gz -d /path/to/midas_database