---
name: "resfinder.py"
section: "1"
platform: "linux"
package: "resfinder"
version: "3.2-3"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/resfinder.py"
---

# resfinder.py(1)

identify acquired antimicrobial resistance genes

## NAME

resfinder.py - identify acquired antimicrobial resistance genes

## SYNOPSIS

**resfinder.py** \[-h\] **-i** INPUTFILE \[INPUTFILE ...\] \[-o OUT\_PATH\] \[-tmp TMP\_DIR\] \[-mp METHOD\_PATH\] \[-p DB\_PATH\] \[-d DATABASES\] \[-l MIN\_COV\] \[-t THRESHOLD\] \[-ao ACQ\_OVERLAP\] \[-matrix\] \[-x\] \[-q\]

## OPTIONS

### optional arguments:

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

  show this help message and exit

- **-i** INPUTFILE \[INPUTFILE ...\], **--inputfile** INPUTFILE \[INPUTFILE ...\]

  FASTA or FASTQ input files.

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

  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 none are specified all are used

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

  Minimum coverage

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

  Blast threshold for identity

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

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

- **-matrix**, **--matrix**

  Gives the counts all all called bases at each position in each mapped template. Columns are: reference base, A count, C count, G count, T count, N count, - count.

- **-x**, **--extended\_output**

  Give extended output with alignment files, template and query hits in fasta and a tab separated file with gene profile results

**-q**, **--quiet**

## AUTHOR

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