---
name: "virulencefinder.py"
section: "1"
platform: "linux"
package: "virulencefinder"
version: "2.0.5-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/virulencefinder.py"
---

# virulencefinder.py(1)

identify virulence genes in total or partial sequenced isolates of bacteria

## 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.