Quick Start

Typical Workflow

CheckM works on a directory of genome bins in FASTA format. By default, CheckM assumes these files end with the extension fna, though this can be changed with the –x flag. CheckM consists of a series of commands in order to support a number of different analyses and workflows. If you are in a rush to get started, the standard workflow for CheckM is:

> checkm lineage_wf <bin folder> <output folder>

For a full list of options, run checkm lineage_wf. To speed up processing, use the -t flag to specify the desired number of threads.

Example Usage

Assume you have putative genomes in the directory /home/donovan/bins with fa as a the file extension and want to store the CheckM results in /home/donovan/checkm. Simply run:

> checkm lineage_wf -t 8 -x fa /home/donovan/bins /home/donovan/checkm