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CheckM container

Main tool: CheckM

Code repository: https://github.com/Ecogenomics/CheckM

Additional tools:

  • HHMER: 3.3.2+dfsg-1
  • prodigal: 1:2.6.3-5
  • pplacer: 1.1.alpha19-0-g807f6f3

Basic information on how to use this tool:

  • executable: checkm
  • help: <-h>
  • version: <-h>
  • description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

Additional information:

This container does not include precalculated data files that CheckM relies on
Those files can be downloaded from either:

The reference data must be decompress into a directory. Inform CheckM of where the files have been placed with the following command:

checkm data setRoot <checkm_database_dir>

Full documentation: https://github.com/Ecogenomics/CheckM/wiki

Example Usage

checkm lineage_wf -t 8 -x fasta input_folder output_folder