recipe midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Homepage

https://github.com/snayfach/MIDAS

License

GPL / GPL-3.0

Recipe

/midas/meta.yaml

package midas

Versions

1.3.2-6,  1.3.2-5,  1.3.2-4,  1.3.2-3,  1.3.2-2,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.2-1, 

1.3.2-6,  1.3.2-5,  1.3.2-4,  1.3.2-3,  1.3.2-2,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.2-1,  1.2.2-0

Depends

• biopython

• bowtie2

• hs-blastn

• numpy

• pandas

• pysam

• python

• samtools >=1.4.0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install midas

and update with:

conda update midas

or use the docker container:

docker pull quay.io/biocontainers/midas:<tag>

(see midas/tags for valid values for <tag>)

Notes

MIDAS requires reference database that needs to be additionally downloaded and set, https://github.com/snayfach/MIDAS/blob/master/docs/ref_db.md.

Link to this page

Render an badge with the following MarkDown:

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