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.

For more information, please check the CheckM Wiki page.

d__ = Domain
p__ = Phylum
c__ = Class
o__ = Order
f__ = Family
g__ = Genus
s__ = Species
st__ = Strain
x__ = No rank

The NCBI taxonomy is as described in the current RefSeq release used by GTDB, which may not be the latest RefSeq release available at the NCBI website.

The information on this table has been parsed from the NCBI FTP website.

Go to the NCBI Page