Main tool: checkv
Code repository: https://bitbucket.org/berkeleylab/checkv/
Additional tools:
- diamond: 2.1.8
- prodigal-gv: 2.11.0
- hmmer: 3.3.2
- blast: 2.12.0+
Basic information on how to use this tool:
- executable: checkv
- help: -h
- version:
- description:
CheckV is the first fully automated, command-line tool for assessing the quality of metagenome-assembled viral genomes
Additional information:
This container does not include any database. You can use checkv download_database command or https://portal.nersc.gov/CheckV/ address to download it manually
Full documentation: https://bitbucket.org/berkeleylab/checkv/src/master/
# Using a single command to run the full pipeline (recommended)
checkv end_to_end input_file.fna output_directory -t 16
# Using individual commands for each step in the pipeline
checkv contamination input_file.fna output_directory -t 16
checkv completeness input_file.fna output_directory -t 16
checkv complete_genomes input_file.fna output_directory
checkv quality_summary input_file.fna output_directory