Skip to content

CheckM

CheckM is a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Two variants are available: the first packages version 1.2.4 of CheckM, and the second packages version 1.1.0 of CheckM2.

Usage example

Run module load checkm to load the CheckM2 release. Once loaded, the module makes the checkm2 command available. Alternatively, run module load checkm release=1 to load the CheckM release and make the checkm command available.

The checkm_shell command can be used to access a shell in the bundle.

Run pet list -t checkm for a list of examples.

Performance notes

No performance notes available

CheckM should be run on a system with at least 64 GB of RAM and 16 threads.

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

CheckM1 is licensed under the GPLv3 license. and CheckM2 is licensed under the GPLv3 license.

Primary citation

  • CheckM1

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043-1055.

  • CheckM2

Chklovski, A., Parks, D.H., Woodcroft, B.J. et al. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 20, 1203–1212 (2023). doi

External guides and resources

  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za