CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.



The CheckM dataset is available on Bridges as /pylon5/datasets/community/checkm.


To see what versions of CheckM are available type

module avail checkm

To see what other modules are needed, what commands are available and how to get additional help type

module help  checkm

To use CheckM, include a command like this in your batch script or interactive session to load the checkm module:

module load checkm


Be sure you also load any other modules needed, as listed by the module help checkm command.