Installer chopper avec Homebrew

Liens du projet

• Page d'accueil

Commandes et alias

• chopper

Historique du projet

The project's GitHub repository was created in August 2020. Its first published GitHub release was v0.1.0 in November 2022, and development has continued through later releases that expanded its filtering and trimming strategies.

Historique d'adoption

The project distributes ready-to-use binaries from GitHub Releases and documents installation through Bioconda. The supplied package metadata also records a Homebrew formula, making it available in both bioinformatics-focused and general-purpose package-manager workflows.

Modes d'utilisation

chopper fits Unix sequencing pipelines by reading FASTQ from standard input and writing accepted reads to standard output. Common invocations set minimum quality and length thresholds, optionally crop or quality-trim reads, and pipe compressed data through gzip or pigz.

Pourquoi les passionnés de paquets s'y intéressent

For package-oriented users, chopper is notable as a small Rust replacement for older Python tooling that preserves stream-based composition while offering standalone release binaries and Bioconda and Homebrew distribution. Its stdin/stdout interface makes it easy to slot into reproducible shell pipelines without project-specific configuration.

Chronologie

• 2020: GitHub repository created.
• 2022: First GitHub release, v0.1.0.
• 2026: v0.13.0 released with split-window support for low-quality splitting.

Related projects

• NanoFilt and NanoLyse are the Python tools whose functionality motivated chopper's Rust implementation.
• pigz is recommended in the official README for overlapping FASTQ compression or decompression with chopper's processing.

Sources

• https://api.github.com/repos/wdecoster/chopper
• https://api.github.com/repos/wdecoster/chopper/releases?per_page=100
• https://github.com/wdecoster/chopper#readme
• source_facts.package-manager