# Install fastp with Homebrew, apt, Nix Ultra-fast all-in-one FASTQ preprocessor. Version 1.3.6 via Homebrew; verified 2026-06-29. ## Install ```sh sudo av install brew:fastp ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install fastp ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install fastp ``` Evidence: Debian stable package indexes: fastp from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#fastp ``` Evidence: nixpkgs package indexes: pkgs/by-name/fa/fastp/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:fastp - **Package manager:** Homebrew - **Package manager page:** - **Version:** 1.3.6 - **Source summary:** Ultra-fast all-in-one FASTQ preprocessor - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Last updated:** 2026-06-29T10:45:23Z - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - fastp (cli) - fastp (alias) ## Dependencies - highway - isa-l - libdeflate ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 1.3.6 - Package-manager updated: 2026-06-29 - Local data: ok - Upstream repository: https://github.com/OpenGene/fastp - Upstream latest detected: v1.3.6 (current) ## 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. ### Sources - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** fastp - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Debian apt - fastp - 0.24.0+dfsg-1: normalized package name match | Debian stable package indexes: fastp from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Ultra-fast all-in-one FASTQ preprocessor | https://github.com/OpenGene/fastp - Nix - fastp: normalized package name match | nixpkgs package indexes: pkgs/by-name/fa/fastp/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - fastp - 0.23.4+dfsg-1: normalized package name match | Ubuntu 24.04 LTS package indexes: fastp from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Ultra-fast all-in-one FASTQ preprocessor | https://github.com/OpenGene/fastp ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [isa-l](https://www.automicvault.com/pkg/brew/isa-l/) - Runtime dependency declared by Homebrew. - [libdeflate](https://www.automicvault.com/pkg/brew/libdeflate/) - Runtime dependency declared by Homebrew. - [fastq-tools](https://www.automicvault.com/pkg/brew/fastq-tools/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [rasusa](https://www.automicvault.com/pkg/brew/rasusa/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastqc](https://www.automicvault.com/pkg/brew/fastqc/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, quality-control, science. - [sickle](https://www.automicvault.com/pkg/brew/sickle/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. ## Combined YAML source View the package source record on GitHub. [combined/fastp.yml](https://github.com/automic-vault/db/blob/main/combined/fastp.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph