install

Additional install commands

macOS

Homebrewverified · 100%

brew install chopper

local Homebrew formula metadata

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

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

security posture

No protected-tool coverage found yet

No matching local secret-handling manifest was found for chopper. Package metadata is still published here so future coverage has a stable package URL.

Install behavior

No Homebrew post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Build metadata lists 2 build 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

Command	Kind	Exposure	Note
`chopper`	cli	global 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 generated2026-08-04

manager version0.13.0

manager updated2026-07-15

local dataok

upstreamcurrent

latest detectedv0.13.0

https://github.com/wdecoster/chopper

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:chopper
Version	0.13.0
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/chopper
Homepage	https://github.com/wdecoster/chopper
Repository	https://github.com/wdecoster/chopper
License	MIT
Source archive	https://github.com/wdecoster/chopper/archive/refs/tags/v0.13.0.tar.gz
Last updated	2026-07-15T10:09:42Z
Pulse	updated
Build dependencies	cmake, rust
Bottle	available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	not defined
Service	none declared

registry facts

Source database details

Source Database	Homebrew formula API
Tap	homebrew/core
Full Name	chopper
Version Scheme	0
Revision	0
Head Version	HEAD
Bottle Stable Root URL	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	head stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

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.

combined/chopper.yml

Used sources

cross-ecosystem install command graph
curated package history
package relationship graph
package version freshness
package-page enrichment
pkg.so package database
pkgdb category and tag curation

Install chopper with Homebrew