Main tool: CheckM
Code repository: https://github.com/Ecogenomics/CheckM
Additional tools:
- HHMER: 3.3.2
- prodigal: 2.6.3
- 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
checkm lineage_wf -t 8 -x fasta input_folder output_folder