# Install cutadapt with Homebrew, apt

Removes adapter sequences from sequencing reads. Version 5.2 via Homebrew; verified 2026-05-04.

## Install

```sh
sudo av install brew:cutadapt
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install cutadapt
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install cutadapt
```

  Evidence: Debian stable package indexes: cutadapt from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

## Package facts

- **Package key:** brew:cutadapt
- **Package manager:** Homebrew
- **Package manager page:** <https://formulae.brew.sh/formula/cutadapt>
- **Version:** 5.2
- **Source summary:** Removes adapter sequences from sequencing reads
- **Homepage:** <https://cutadapt.readthedocs.io>
- **Repository:** <https://github.com/marcelm/cutadapt>
- **Upstream docs:** <https://cutadapt.readthedocs.io/>
- **License:** MIT
- **Source archive:** <https://github.com/marcelm/cutadapt.git>
- **Last updated:** 2026-05-04T20:29:09Z
- **Generated:** 2026-07-08T07:18:31+00:00

## Executables

- cutadapt (cli)
- cutadapt (alias)

## Dependencies

- python@3.14

## Install behavior

- Post-install hook: not defined
- Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## Freshness

- Page generated: 2026-07-08
- Package-manager version: 5.2
- Package-manager updated: 2026-05-04
- Local data: ok
- Upstream repository: https://github.com/marcelm/cutadapt
- info: No cached GitHub release or tag data was available.
## Project history and usage

Cutadapt is a bioinformatics command-line tool for finding and removing adapter sequences, primers, poly-A tails, and other unwanted sequence from high-throughput sequencing reads. Its documentation presents trimming as a routine cleanup step for small-RNA, amplicon, and other sequencing workflows.

### Project history

The project documentation says Cutadapt development began at TU Dortmund University in Prof. Sven Rahmann's group and is now developed within NBIS, the National Bioinformatics Infrastructure Sweden. The documentation copyright begins in 2010, and the changelog records early public releases starting with v0.1 in September 2010.

### Adoption history

Cutadapt became part of the standard sequencing-preprocessing toolbox because it solves a common, format-heavy cleanup problem with a scriptable CLI. The official README links to PyPI, source code, documentation, and a Galaxy platform wrapper, and its badges point to Python packaging and Bioconda distribution.

### How it is used

The tool is normally used in pipelines before alignment or downstream analysis: users provide FASTQ/FASTA reads and adapter or primer patterns, then ask Cutadapt to trim, filter, modify, demultiplex, and report results. Its changelog shows long-running attention to paired-end reads, JSON reports, demultiplexing, compression speed, Python version support, and reproducible output.

### Why package nerds care

Cutadapt is package-manager significant because it bridges Python packaging, bioinformatics channels, and Unix CLI workflows. It is both a Python package and a command-line executable, with stable documentation, a citation, and a long changelog that makes downstream packaging and reproducibility work tractable.

### Timeline

- 2010: v0.1 appears in the official changelog.
- 2011: v1.0 released, according to the changelog.
- 2012: Public GitHub repository created.
- 2019: v2.0 released with documented backward-incompatible changes.
- 2024: v5.0 released with demultiplexing behavior changes and performance-related defaults.
- 2025: v5.2 documented in the stable changelog.

### Related projects

- The official README links Cutadapt to PyPI, Bioconda packaging, Galaxy's tools-iuc wrapper, and its Read the Docs documentation.

### Sources

- <https://cutadapt.readthedocs.io/>
- <https://cutadapt.readthedocs.io/en/stable/changes.html>
- <https://raw.githubusercontent.com/marcelm/cutadapt/main/README.rst>
- <https://api.github.com/repos/marcelm/cutadapt>


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Source Database Details

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** cutadapt
- **Version Scheme:** 0
- **Revision:** 0
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** stable

## Other Package-Manager Records

- Debian apt - cutadapt - 4.7-2: normalized package name match | Debian stable package indexes: cutadapt from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Clean biological sequences from high-throughput sequencing reads | https://cutadapt.readthedocs.io/
- Ubuntu apt - cutadapt - 4.4-1build2: normalized package name match | Ubuntu 24.04 LTS package indexes: cutadapt from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Clean biological sequences from high-throughput sequencing reads | https://cutadapt.readthedocs.io/


## Related links

- [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Language runtime packages](https://www.automicvault.com/pkg/language-runtime-packages/) - Matched language runtime, compiler, or interpreter metadata.
- [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [python@3.14](https://www.automicvault.com/pkg/brew/python-3-14/) - Runtime dependency declared by Homebrew.
- [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: adapter-trimming, bioinformatics, cli, science, sequencing.
- [fgbio](https://www.automicvault.com/pkg/brew/fgbio/) - Shares av.db curated category or tags: bioinformatics, cli, ngs, science, sequencing.
- [sickle](https://www.automicvault.com/pkg/brew/sickle/) - Shares av.db curated category or tags: bioinformatics, cli, ngs, science, sequencing.
- [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [btllib](https://www.automicvault.com/pkg/brew/btllib/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [fastp](https://www.automicvault.com/pkg/brew/fastp/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [flye](https://www.automicvault.com/pkg/brew/flye/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, python, python-3-14, reads.
- [spades](https://www.automicvault.com/pkg/brew/spades/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, python, python-3-14, science.

## Combined YAML source

View the package source record on GitHub. [combined/cutadapt.yml](https://github.com/automic-vault/db/blob/main/combined/cutadapt.yml)


## Sources

- Nucleus package database
- Geiger risk classifier
- package-page enrichment
- curated package history
- package version freshness
- av.db category and tag curation
- package relationship graph
- external package-manager database matches
- cross-ecosystem install command graph