virulencefinder.py - identify virulence genes in total or partial sequenced isolates of bacteria

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

virulencefinder.py 2.0.4                            July 2021                              VIRULENCEFINDER.PY(1)

       usage: virulencefinder.py [-h] -i INFILE [INFILE ...] [-o OUTDIR]

       [-tmp TMP_DIR] [-mp METHOD_PATH] [-p DB_PATH]
              [-d DATABASES] [-l MIN_COV] [-t THRESHOLD] [-x] [--speciesinfo_json SPECIESINFO_JSON] [-q]

   optionalarguments:-h, --help
              show this help message and exit

       -i INFILE [INFILE ...], --infile INFILE [INFILE ...]
              FASTA or FASTQ input files.

       -o OUTDIR, --outputPath OUTDIR
              Path to blast output

       -tmp TMP_DIR, --tmp_dir TMP_DIR
              Temporary directory for storage of the results from the external software.

       -mp METHOD_PATH, --methodPath METHOD_PATH
              Path to method to use (kma or blastn)

       -p DB_PATH, --databasePath DB_PATH
              Path to the databases

       -d DATABASES, --databases DATABASES
              Databases chosen to search in - if non is specified all is used

       -l MIN_COV, --mincov MIN_COV
              Minimum coverage

       -t THRESHOLD, --threshold THRESHOLD
              Minimum hreshold for identity

       -x, --extented_output
              Give  extented  output with allignment files, template and query hits in fasta and a tab seperated
              file with gene profile results

       --speciesinfo_json SPECIESINFO_JSON
              Argument used by the cge pipeline. It takes a list in json format  consisting  of  taxonomy,  from
              domain -> species. A database is chosen based on the taxonomy.

       -q, --quiet

       virulencefinder.py - identify virulence genes in total or partial sequenced isolates of bacteria