Overview

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.

News

  • CheckM v1.1.6 was released on April 9, 2022 and requires Python 3.

Use CheckM

Before using CheckM you need a set of putative genomes. These may come from isolates, single cells, or metagenomic data. Our companion tool GroopM can be used to recover genomes from metagenomic data.

For information on using CheckM visit the wiki.

Cite CheckM

If you find this software useful, we'd love for you to cite us:

Talk to us

We'd love to hear from you. All comments and suggestions can be sent to Donovan Parks:

  • donovan_dot_parks_at_gmail_dot_com

Licensing

CheckM is licensed using the GNU General Public License version 3 as published by the Free Software Foundation.

The CheckM logo is a product of Mike Imelfort's mind.

This site was created using a template created by the wonderful people at bootswatch.