What it does

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.

This command runs recommended workflow to analyze all genome bins with the same marker set. A common example would be a set of genomes from the same taxonomic group.

The workflow for using a taxonomic-specific marker set consists of 3 mandatory (M) steps and 1 recommended (R) step:

• 18. The taxon_list command produces a table indicating all taxa for which a marker set can be produced. All support taxa at a given taxonomic rank can be produced by passing taxon_list the --rank flag
• 13. The taxon_set command is used to produce marker sets for a specific taxon:
• 13. The analyze command identifies marker genes within each genome bin and estimate completeness and contamination. All putative genomes to be analyzed must be provided.
• 13. The qa command is used to produce different tables summarizing the quality of each genome bin.

Inputs

Outputs