Installer fastp avec Homebrew, apt, Nix

Liens du projet

• Page d'accueil
• Docs amont
• Page du gestionnaire de paquets

Commandes et alias

• fastp

Historique du projet

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.

Historique d'adoption

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.

Modes d'utilisation

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.

Pourquoi les passionnés de paquets s'y intéressent

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.

Chronologie

• 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

• https://github.com/OpenGene/fastp
• https://github.com/OpenGene/fastp#readme
• https://doi.org/10.1093/bioinformatics/bty560
• https://doi.org/10.1002/imt2.70078
• https://api.github.com/repos/OpenGene/fastp/releases