---
name: "run_resfinder.py"
section: "1"
platform: "linux"
package: "resfinder"
version: "4.4.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/run_resfinder.py"
---

# run\_resfinder.py(1)

identify acquired antimicrobial resistance genes

## NAME

run\_resfinder.py - identify acquired antimicrobial resistance genes

## DESCRIPTION

usage: run\_resfinder.py \[-h\] \[-ifa INPUTFASTA\]

- \[-ifq INPUTFASTQ \[INPUTFASTQ ...\]\] \[-o OUT\_PATH\]

  \[-b BLAST\_PATH\] \[-k KMA\_PATH\] \[-s SPECIES\] \[-db\_res DB\_PATH\_RES\] \[-db\_res\_kma DB\_PATH\_RES\_KMA\] \[-d DATABASES\] \[-acq\] \[-ao ACQ\_OVERLAP\] \[-l MIN\_COV\] \[-t THRESHOLD\] \[-c\] \[-db\_point DB\_PATH\_POINT\] \[-db\_point\_kma DB\_PATH\_POINT\_KMA\] \[-g SPECIFIC\_GENE \[SPECIFIC\_GENE ...\]\] \[-u\] \[-l\_p MIN\_COV\_POINT\] \[-t\_p THRESHOLD\_POINT\] \[--pickle\]

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-ifa** INPUTFASTA, **--inputfasta** INPUTFASTA

  Input fasta file.

- **-ifq** INPUTFASTQ \[INPUTFASTQ ...\], **--inputfastq** INPUTFASTQ \[INPUTFASTQ ...\]

  Input fastq file(s). Assumed to be single-end fastq if only one file is provided, and assumed to be pairedend data if two files are provided.

- **-o** OUT\_PATH, **--outputPath** OUT\_PATH

  Path to blast output

- **-b** BLAST\_PATH, **--blastPath** BLAST\_PATH

  Path to blastn

- **-k** KMA\_PATH, **--kmaPath** KMA\_PATH

  Path to KMA

- **-s** SPECIES, **--species** SPECIES

  Species in the sample

- **-db\_res** DB\_PATH\_RES, **--db\_path\_res** DB\_PATH\_RES

  Path to the databases for ResFinder

- **-db\_res\_kma** DB\_PATH\_RES\_KMA, **--db\_path\_res\_kma** DB\_PATH\_RES\_KMA

  Path to the ResFinder databases indexed with KMA. Defaults to the 'kma\_indexing' directory inside the given database directory.

- **-d** DATABASES, **--databases** DATABASES

  Databases chosen to search in - if none is specified all is used

- **-acq**, **--acquired**

  Run resfinder for acquired resistance genes

- **-ao** ACQ\_OVERLAP, **--acq\_overlap** ACQ\_OVERLAP

  Genes are allowed to overlap this number of nucleotides. Default: 30.

- **-l** MIN\_COV, **--min\_cov** MIN\_COV

  Minimum (breadth-of) coverage of ResFinder

- **-t** THRESHOLD, **--threshold** THRESHOLD

  Threshold for identity of ResFinder

- **-c**, **--point**

  Run pointfinder for chromosomal mutations

- **-db\_point** DB\_PATH\_POINT, **--db\_path\_point** DB\_PATH\_POINT

  Path to the databases for PointFinder

- **-db\_point\_kma** DB\_PATH\_POINT\_KMA, **--db\_path\_point\_kma** DB\_PATH\_POINT\_KMA

  Path to the PointFinder databases indexed with KMA. Defaults to the 'kma\_indexing' directory inside the given database directory.

- **-g** SPECIFIC\_GENE \[SPECIFIC\_GENE ...\]

  Specify genes existing in the database to search for - if none is specified all genes are included in the search.

- **-u**, **--unknown\_mut**

  Show all mutations found even if in unknown to the resistance database

- **-l\_p** MIN\_COV\_POINT, **--min\_cov\_point** MIN\_COV\_POINT

  Minimum (breadth-of) coverage of Pointfinder. If None is selected, the minimum coverage of ResFinder will be used.

- **-t\_p** THRESHOLD\_POINT, **--threshold\_point** THRESHOLD\_POINT

  Threshold for identity of Pointfinder. If None is selected, the minimum coverage of ResFinder will be used.

- **--pickle**

  Create a pickle dump of the Isolate object. Currently needed in the CGE webserver. Dependency and this option is being removed.

## AUTHOR

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