NAME

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

DESCRIPTION

       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]

   optional arguments:
       -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

AUTHOR

        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)