---
name: "seqtk"
section: "1"
platform: "linux"
package: "seqtk"
version: "1.4-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/seqtk"
---

# seqtk(1)

sampling, trimming, fastq2fasta, subsequence, reverse complement

## NAME

seqtk - sampling, trimming, fastq2fasta, subsequence, reverse complement

## SYNOPSIS

**seqtk** *\<command\> \<arguments\>*

## DESCRIPTION

Currently, seqtk supports quality based trimming with the phred algorithm, converting fastq to fasta, reverse complementing sequences, extracting or masking subsequences in regions given in a BED/name list file, and more.  It contains a subsampling module to sample exactly n sequences or a fraction of sequences.

Seqtk supports both fasta and fastq input files, which can be optionally gzip compressed.

## COMMANDS

Command: seq       common transformation of FASTA/Q

- *comp*

  get the nucleotide composition of FASTA/Q

- *sample*

  subsample sequences

- *subseq*

  extract subsequences from FASTA/Q

- *trimfq*

  trim FASTQ using the Phred algorithm

- *hety*

  regional heterozygosity

- *mutfa*

  point mutate FASTA at specified positions

- *mergefa*

  merge two FASTA/Q files

- *randbase*

  choose a random base from hets

- *cutN*

  cut sequence at long N

- *listhet*

  extract the position of each het