---
name: "plasmidseeker"
section: "1"
platform: "linux"
package: "plasmidseeker"
version: "1.3+dfsg-3+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/plasmidseeker"
---

# plasmidseeker(1)

identification of known plasmids from whole-genome sequencing reads

## NAME

plasmidseeker - identification of known plasmids from whole-genome sequencing reads

## SYNOPSIS

**plasmidseeker** *-d \<PLASMID DB DIR\> -i \<SAMPLE.fastq\> -b \<CLOSEST BACTERIA TO ISOLATE\> -o \<OUTPUT FILE\>*

## OPTIONS

- **-i**

  Input fastq file

- **-o**

  Output file name (default plasmidseeker\_result.txt)

- **-d**

  Path to plasmid database directory

- **-b**

  Closest bacteria to isolate genome fna

- **-t**

  Number of threads used (default 32)

- **-f**

  Minimum threshold F - at least this fraction of unique k-mers that has to be found for a plasmid (default 80)

- **-h**

  Print this help

- **--verbose**

  Print out more working process

- **--ponly**

  Assumes that reads contain only plasmid sequences (use for extracted plasmids)

- **-v**

  Print version of the program

## AUTHOR

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