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



  • CheckM home on GitHub
  • If you use CheckM in your research, please cite:
    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043–1055.



The CheckM dataset is available on Bridges-2 as /ocean/datasets/community/genomics/checkm/latest.


To see what versions of CheckM are available, and which is the default if there is more than one, type:

module spider checkm

To see what other modules are needed, what commands are available and how to get additional help type (note that the module help command is case-sensitive):

module help CheckM

To use CheckM, include a command like this in your batch script or interactive session to load the CheckM module (note that the module load command is case-sensitive):

module load CheckM