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brew install chopperlocal Homebrew formula metadata
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Install chopper with Homebrew
Filter and trim long-read sequencing data by quality and length. Version 0.13.0 via Homebrew; verified 2026-07-15.
install
Additional install commands
overview
Package summary
Filter and trim long-read sequencing data by quality and length
Project links
Commands and aliases
- chopper
history
Project history and usage
chopper is a Rust command-line program for filtering and trimming FASTQ reads from long-read sequencing platforms such as Oxford Nanopore and PacBio. It is designed as a faster reimplementation of functionality associated with the Python tools NanoFilt and NanoLyse.
Project history
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.
Adoption history
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.
How it is used
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.
Why package nerds care
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.
Timeline
- 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
security posture
No protected-tool coverage found yet
No matching local secret-handling manifest was found for chopper. Nucleus package metadata is still published here so future coverage has a stable package URL.
Install behavior
- No Homebrew bottle metadata was recorded.
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
| Command | Kind | Exposure | Note |
|---|---|---|---|
chopper | executable | indexed executable | Discovered from the local executable index. |
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 generated2026-08-03
manager version0.13.0
manager updated2026-07-15
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:chopper |
|---|---|
| Version | 0.13.0 |
| Package manager | Homebrew |
| Homepage | https://github.com/wdecoster/chopper |
| Repository | https://github.com/wdecoster/chopper |
| Last updated | 2026-07-15T10:09:42Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
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.
Combined YAML source
View the package source record on GitHub.
Used sources
- cross-ecosystem install command graph
- curated package history
- pkg.so package database
- pkgdb category and tag curation