CheckM2

CheckM2 uses machine learning to rapidly assess the quality of assembled genome bins. It uses two different models to predict the completeness of the binned genomes. Please see the source page, listed below, for more information.

Using the module

To load CheckM2 in an interactive session on Palmetto:

module load biocontainers
module load checkm2

After loading the biocontainers module, you can see the available commands by running:

report_subtools.sh checkm2

Example

For reference, the CheckM2 database is located at /datasets/CheckM2_database/

An example analysis command could look as follows:

checkm2 predict --threads $SLURM_CPUS_ON_NODE --input <folder_with_bins> --output-directory <output_folder>

tip

This software has multithreading features! Please try to request additional resources to expedite your analyses! Remember to set the --threads flag accordingly!

Please see CheckM2 source page for more information.

Parallel Capabilities: Single core default, multithreading options available.