# 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

```sh
sudo av install brew:chopper
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install chopper
```

  Evidence: local Homebrew formula metadata

## Package facts

- **Package key:** brew:chopper
- **Package manager:** Homebrew
- **Version:** 0.13.0
- **Source summary:** Filter and trim long-read sequencing data by quality and length
- **Homepage:** <https://github.com/wdecoster/chopper>
- **Repository:** <https://github.com/wdecoster/chopper>
- **Last updated:** 2026-07-15T10:09:42Z
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- chopper (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 0.13.0
## 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 Notes

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.



## Combined YAML source

View the package source record on GitHub. [combined/chopper.yml](https://github.com/mxcl/pkgdb/blob/main/combined/chopper.yml)


## Sources

- pkg.so package database
- curated package history
- pkgdb category and tag curation
- cross-ecosystem install command graph