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.
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.
If you find this software useful, we'd love for you to cite us:
We'd love to hear from you. All comments and suggestions can be sent to Donovan Parks:
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.
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