CheckM

CheckM is a command-line software tool used to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. It provides quantitative estimates of genome completeness and contamination, along with related metrics, to help researchers evaluate the reliability of genome bins and assemblies.

The core method of CheckM relies on lineage-specific marker genes. It detects a curated set of single-copy marker genes expected to occur once within a lineage. By examining the presence, absence, and copy number of these markers, CheckM estimates how complete a genome is and how much foreign sequence may be present in a bin. It also reports strain heterogeneity, an indicator of mixed populations within a bin, and flags potential chimeric assemblies.

CheckM employs a lineage-aware workflow. It places a genome bin into a reference lineage tree and selects the appropriate marker gene set for that lineage, enabling more accurate quality estimates across diverse taxa. The tool can work with assembled contigs or whole genomes and is designed to handle bins from metagenomic assemblies as well as single-cell amplified genomes. Outputs typically include completeness and contamination percentages, strain heterogeneity, taxonomic placement, and a quality score used for filtering in downstream analyses.

Availability and impact: CheckM is open source and widely used in microbial genomics. It has become a standard component of quality control in binning pipelines and genome-resolved metagenomics, helping researchers curate high-quality genomes for comparative analyses and downstream functional studies.