CheckM

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. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

CheckM is open source and released under the GNU General Public License (Version 3). The source code is available on GitHub.

CheckM v2 has been released

Important

CheckM v2 has been released and can be found at https://github.com/chklovski/CheckM2. CheckM v1 (documented here) estimates genome completeness and contamination based on the presence or absence of marker genes, i.e., genes that are typically ubiquitous and single copy. In contrast, CheckM v2 uses machine learning models to estimate completeness and contamination. Our assessment indicates CheckM v2 will be more accurate in general. However, you may consider running both CheckM v1 and v2 in some cases since these are independent methodologies for estimating genome quality. It can also be insightful to explore the marker genes that are missing in your genomes, especially if you have multiple related genomes and are interested in systematic loss of an otherwise ubiquitous gene.

Outside of minor updates to fix compatibility issues with external dependencies, no maintenance is intended for CheckM v1.

Latest release

The latest release of CheckM is 1.3.0. See the Change log for the changes in each release.

CheckM >= 1.3.0 requires Python >= 3.11. We do not recommend installing CheckM from the master branch, which may be unstable. Please install an official release of CheckM (see Installing CheckM).

Running CheckM

  1. Install CheckM and its reference data (Installing CheckM).

  2. Run the lineage-specific workflow on a directory of genomes (Quick start):

    checkm lineage_wf -t 8 -x fa <bin folder> <output folder>

  3. See Workflows for the available workflows, Commands for all commands, and Outputs for a description of the reported statistics. A list of commands is also shown by running checkm (or checkm -h), and help for an individual command by running checkm <command> -h.

Information about obtaining improved quality estimates for CPR (Patescibacteria) genomes can be found in Using the CPR marker set.

Please report bugs through the GitHub issues system (see FAQ and support).

Citing CheckM

If you use CheckM in your research, please cite CheckM and the software it relies on, as described in Citing CheckM.

Getting started

Running CheckM

About

Additional information