g# geNomad container
Main tool: geNomad
Code repository: https://github.com/apcamargo/genomad/
Additional tools:
- aragorn: 1.2.41
- mmseq2: 15-6f452
Basic information on how to use this tool:
- executable: genomad
- help: --help
- version: --version
- description: Identification of mobile genetic elements
Additional information:
The geNomad database version 1.7 is downloaded in /genomad_db.
Full documentation: https://portal.nersc.gov/genomad/
# to download the database (database is already downloaded at /genomad_db)
genomad download-database .
# recommended usage
genomad end-to-end input.fna output /genomad_db
# subsections of genomad
genomad annotate metagenome.fna genomad_output /genomad_db
genomad find-proviruses metagenome.fna genomad_output /genomad_db
genomad marker-classification metagenome.fna genomad_output /genomad_db
genomad nn-classification metagenome.fna /genomad_output
genomad aggregated-classification metagenome.fna /genomad_output
genomad score-calibration metagenome.fna /genomad_output
genomad summary metagenome.fna /genomad_output