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Quick Start
Donovan Parks edited this page Jun 16, 2014
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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>
Assume you have genome bins in the directory /home/donovan/my_project/bins
with fa
as an extension and want to store the CheckM results in /home/donovan/my_project/checkm
, simply run:
> checkm lineage_wf -x fa /home/donovan/my_project/bins /home/donovan/my_project/checkm