pkg.soopen package index

brew / rank 5171

Install seqtk with Homebrew, apt, Nix

Toolkit for processing sequences in FASTA/Q formats. Version 1.5 via Homebrew; verified 2026-09-11. Also installable with debian: sudo apt install seqtk.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install seqtk

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install seqtk

Debian stable package indexes · seqtk · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#seqtk

nixpkgs package indexes · pkgs/by-name/se/seqtk/package.nix · source: api.github.com

overview

Package summary

Toolkit for processing sequences in FASTA/Q formats

Commands and aliases

  • seqtk

history

Project history and usage

Seqtk is a lightweight command-line toolkit for common transformations and selections on FASTA and FASTQ biological-sequence files.

Project history

Seqtk was created by Heng Li as a fast, lightweight toolkit for manipulating FASTA and FASTQ sequence data. Its implementation and build remain deliberately small, with zlib as its only library dependency.

Adoption history

Seqtk is distributed by multiple Unix package ecosystems, including Homebrew, Debian, Ubuntu, and Nix, making its small command-line toolkit readily available in bioinformatics environments.

How it is used

Typical uses include FASTQ-to-FASTA conversion, reverse complementation, sequence or region extraction, masking, paired-read subsampling, quality trimming, and line normalization. It accepts gzip-compressed input and is commonly placed in shell pipelines.

Why package nerds care

Seqtk is valued as a compact, zlib-only sequence-processing utility that composes naturally with pipes and established genomics tools. Its focused executable covers many routine FASTA/FASTQ transformations without requiring a larger workflow framework.

Timeline

  • 2010s: Seqtk became a commonly packaged Unix command-line utility for lightweight FASTA/FASTQ processing.

Related projects

  • Seqtk commonly appears alongside read aligners and other command-line genomics software that consume FASTA, FASTQ, BED, or related formats.

Sources

  • Official repository and README: https://github.com/lh3/seqtk
  • source_facts.package-manager

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
seqtkcliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-09-19
manager version1.5
manager updated2026-09-11
local dataok
upstreamcurrent
latest detectedv1.5

https://github.com/lh3/seqtk

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:seqtk
Version1.5
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/seqtk
Homepagehttps://github.com/lh3/seqtk
Repositoryhttps://github.com/lh3/seqtk
LicenseMIT
Source archivehttps://github.com/lh3/seqtk/archive/refs/tags/v1.5.tar.gz
Last updated2026-09-11T16:43:42Z
Pulseupdated
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Nameseqtk
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

seqtk 1.4-2

Fast and lightweight tool for processing sequences in the FASTA or FASTQ format

https://github.com/lh3/seqtk

sudo apt install seqtk
  • Section: science
  • Architecture: amd64
  • 2 dependencies
  • normalized package name match
  • Matched by: Seqtk
Debian stable package indexes · deb.debian.org · Debian stable package indexes: seqtk from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

seqtk

nix profile install nixpkgs#seqtk
  • normalized package name match
  • Matched by: Seqtk
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/se/seqtk/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

seqtk 1.4-2

Fast and lightweight tool for processing sequences in the FASTA or FASTQ format

https://github.com/lh3/seqtk

sudo apt install seqtk
  • Section: universe/science
  • Architecture: amd64
  • 2 dependencies
  • normalized package name match
  • Matched by: Seqtk
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: seqtk from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Same workflow

  • seqkitShares pkgdb curated category or tags: bioinformatics, cli, fasta, fastq, science.
  • mmseqs2Shares pkgdb curated category or tags: bioinformatics, cli, science, sequence-analysis.
  • fastqcShares pkgdb curated category or tags: bioinformatics, cli, fastq, science.
  • fastpShares pkgdb curated category or tags: bioinformatics, cli, fastq, science.
  • kalignShares pkgdb curated category or tags: bioinformatics, cli, science, sequence-analysis.
  • proteinorthoShares pkgdb curated category or tags: bioinformatics, cli, science, sequence-analysis.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment
  • pkg.so package database
  • pkgdb category and tag curation