Automic VaultAutomic Vault

brew

Install fastp with Homebrew, apt, Nix

Ultra-fast all-in-one FASTQ preprocessor. Version 1.3.6 via Homebrew; verified 2026-06-29.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install fastp

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install fastp

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

Nixverified · 92%
nix profile install nixpkgs#fastp

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

overview

Package summary

Ultra-fast all-in-one FASTQ preprocessor

Commands and aliases

  • fastp

history

Project history and usage

fastp is an all-in-one FASTQ preprocessor for short-read sequencing data. It combines quality control, filtering, adapter trimming, per-read cutting, UMI handling, paired-end merging, and HTML/JSON reporting in one command-line tool.

Project history

The OpenGene fastp repository was created in 2017, and the original fastp paper appeared in Bioinformatics in 2018. The project described itself as an ultra-fast all-in-one FASTQ preprocessor at a time when many pipelines chained separate QC, trimming, and filtering tools.

The README documents continuing expansion after the original release: batch processing, STDIN/STDOUT streaming, output splitting for parallel processing, polyG/polyX trimming, UMI processing, duplication analysis, and support for modern dependencies such as ISA-L, libdeflate, and Google Highway. A 2025 iMeta paper is listed by the project as the fastp 1.0 citation.

Adoption history

fastp has broad bioinformatics packaging and workflow adoption signals. Its README advertises Bioconda installation, Debian packaging, and direct use from the European Galaxy server, and the source repository has remained active with releases into 2026.

The tool became popular because it gives sequencing users an immediate before-and-after QC report while also producing cleaned FASTQ files. That made it convenient for command-line pipelines, Galaxy workflows, and package managers that prefer one reproducible executable over a chain of small filters.

How it is used

Typical fastp usage passes input and output FASTQ files with -i/-o for single-end data and -i/-I/-o/-O for paired-end data. By default it writes fastp.html and fastp.json reports, making it useful both as a preprocessing step and as a QC artifact generator.

The README also documents streaming operation, interleaved input, failed-read output, partial processing for quick previews, output splitting, paired-end merging, and automatic adapter handling. No persistent config or credential file is documented.

Why package nerds care

fastp matters to package nerds because it condensed a common NGS preprocessing stack into one fast native binary with reports. The interesting packaging edge is its performance dependency chain: ISA-L, libdeflate, and Highway need to line up cleanly across Linux and macOS builds.

Timeline

  • 2017: The public OpenGene fastp repository is created.
  • 2018: The original Bioinformatics fastp paper is published.
  • 2025: The project lists the fastp 1.0 iMeta paper as the preferred citation.
  • 2026: v1.3.6 is released.

Related projects

  • The README compares fastp reports to FastQC and mentions Trimmomatic-style sliding-window quality cutting. It also points long-read users to OpenGene fastplong.

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.
  • Installs with 3 runtime dependencies.

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
fastpcliglobal 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 generated2026-07-08
manager version1.3.6
manager updated2026-06-29
local dataok
upstreamcurrent
latest detectedv1.3.6

https://github.com/OpenGene/fastp

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:fastp
Version1.3.6
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/fastp
Homepagehttps://github.com/OpenGene/fastp
Repositoryhttps://github.com/OpenGene/fastp
Upstream docshttps://github.com/OpenGene/fastp#readme
LicenseMIT
Source archivehttps://github.com/OpenGene/fastp/archive/refs/tags/v1.3.6.tar.gz
Last updated2026-06-29T10:45:23Z
Pulseupdated
Dependencieshighway, isa-l, libdeflate
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 Namefastp
Version Scheme0
Revision0
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • 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%

fastp 0.24.0+dfsg-1

Ultra-fast all-in-one FASTQ preprocessor

https://github.com/OpenGene/fastp

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

fastp

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

fastp 0.23.4+dfsg-1

Ultra-fast all-in-one FASTQ preprocessor

https://github.com/OpenGene/fastp

sudo apt install fastp
  • Section: universe/science
  • Architecture: amd64
  • 5 dependencies
  • normalized package name match
  • Matched by: Fastp
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: fastp 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.

Related tools

  • isa-lRuntime dependency declared by Homebrew.
  • libdeflateRuntime dependency declared by Homebrew.

Same workflow

  • fastq-toolsShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • rasusaShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • adapterremovalShares av.db curated category or tags: bioinformatics, cli, science, sequencing.
  • fastqcShares av.db curated category or tags: bioinformatics, cli, fastq, quality-control, science.
  • sickleShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • alevin-fryShares av.db curated category or tags: bioinformatics, cli, science, sequencing.

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
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment