Main tool: krocus
Code repository: https://github.com/andrewjpage/krocus
Basic information on how to use this tool:
- executable:
krocus - help:
krocus --help - version:
krocus --version - description: MLST typing from uncorrected long reads
Additional dependencies:
- python 3.10.6
- biopython 1.79
- pyfastaq 3.17.0
This container does not contain any of the mlst schemes. They must be downloaded prior to running the tool.
Full documentation: https://github.com/andrewjpage/krocus
krocus_database_downloader -s "Species" -o allele_directory
krocus allele_directory input.fastq