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CheckM2 container

Main tool: checkm2

Code repository: https://github.com/chklovski/CheckM2

Additional tools:

  • diamond: 2.0.4
  • prodigal 2.6.3

Basic information on how to use this tool:

  • executable: checkm2
  • help: -h, --help
  • version: --version
  • description: Rapid assessment of genome bin quality using machine learning.

Additional information:

CheckM2 relies on a external diamond database (~1.7 GB) for rapid annotation. the database can be downloaded via checkm2 database --download command or obtained directly from: https://zenodo.org/api/records/5571251/files/checkm2_database.tar.gz/content

Full documentation: https://github.com/chklovski/CheckM2

Example Usage

checkm2 predict --threads 8 fasta --input ./input_folder --output-directory ./output_folder --database_path /path/to/database/CheckM2_database/uniref100.KO.1.dmnd