CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage.

• Version: 1.1.2
• Added: March, 2020
• Link: https://ecogenomics.github.io/CheckM/

See which versions of checkm are available:

$ module avail checkm

Load one version into your environment and run it:

$ module load checkm/1.1.2
$ drep

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/checkm/1.1.2
$ sudo chown aorth /export/apps/checkm/1.1.2
$ python3.6 -m venv /export/apps/checkm/1.1.2
$ source /export/apps/checkm/1.1.2/bin/activate
$ pip install --upgrade pip setuptools
$ pip install checkm-genome==1.1.2
$ sudo chown -R root:root /export/apps/checkm/1.1.2