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.
