install

Additional install commands

macOS

Homebrewverified · 100%

brew install cutadapt

local Homebrew formula metadata

Linux

Debian aptverified · 92%

sudo apt install cutadapt

Debian stable package indexes · cutadapt · source: deb.debian.org

overview

Package summary

Removes adapter sequences from sequencing reads

Project links

Commands and aliases

cutadapt

history

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

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

narrow executable package without higher-risk signals

Signals

metadata:no-higher-risk-signals

Install behavior

No Homebrew post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 1 runtime 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
`cutadapt`	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 generated2026-07-08

manager version5.2

manager updated2026-05-04

local dataok

upstreamnot checked

latest detectednot detected

https://github.com/marcelm/cutadapt

infoNo cached GitHub release or tag data was available.https://github.com/marcelm/cutadaptnone confidence

install metadata

Package metadata

Package key	brew:cutadapt
Version	5.2
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/cutadapt
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
Pulse	updated
Dependencies	python@3.14
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	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

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

cutadapt 4.7-2

Clean biological sequences from high-throughput sequencing reads

https://cutadapt.readthedocs.io/

sudo apt install cutadapt

Section: science
Architecture: all
Source Package: python-cutadapt
2 dependencies
normalized package name match
Matched by: Cutadapt

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

Ubuntu apt95%

cutadapt 4.4-1build2

Clean biological sequences from high-throughput sequencing reads

https://cutadapt.readthedocs.io/

sudo apt install cutadapt

Section: universe/science
Architecture: all
Source Package: python-cutadapt
2 dependencies
normalized package name match
Matched by: Cutadapt

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: cutadapt from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

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/cutadapt.yml

Used sources

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

Install cutadapt with Homebrew, apt