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.
