Description

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

analysis_dir (file)

Directory containing output of checkm/analyze or checkm/lineage_wf etc.

*

marker_file (file)

Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf

*.ms

coverage_file (file)

File containing coverage of each sequence (generated by checkm coverage)

exclude_marker_file (file)

File specifying markers to exclude from marker sets

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

output (file)

Default completeness statistics in various formats, as specified with —out_format (excluding option: 9)

*.txt

fasta (file)

Output in fasta format (only if —out_format 9)

*.fasta
included in
mag
author
Github user jfy133
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Tools

checkm
GPL v3

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

ecogenomics.github.io/CheckM github.com/Ecogenomics/CheckM/wiki https://github.com/Ecogenomics/CheckM 10.1101/gr.186072.114