安装

其他安装命令

macOS

Homebrew已验证 · 100%

brew install cutadapt

local Homebrew formula metadata

Linux

Debian apt已验证 · 92%

sudo apt install cutadapt

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

概览

软件包摘要

Removes adapter sequences from sequencing reads

项目链接

命令和别名

cutadapt

历史

项目历史与用法

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.

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

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.

来源

安全态势

风险级别：绿色

narrow executable package without higher-risk signals.

风险分类器

绿色风险 · 低置信度 · appliance

原因

narrow executable package without higher-risk signals

信号

metadata:no-higher-risk-signals

安装行为

formula 元数据中未记录 Homebrew post-install 钩子。
Homebrew bottle 元数据适用于 6 个平台目标。
安装时包含 1 个运行时依赖。

建议审查

在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。

可执行文件

已安装的可执行文件

命令	类型	暴露范围	备注
`cutadapt`	cli	全局可执行文件

新鲜度

版本和新鲜度

这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。

页面生成时间2026-07-08

管理器版本5.2

管理器更新时间2026-05-04

本地数据OK

上游not checked

检测到的最新版本未检测到

https://github.com/marcelm/cutadapt

信息No cached GitHub release or tag data was available.https://github.com/marcelm/cutadaptnone 置信度

安装元数据

软件包元数据

软件包键	brew:cutadapt
版本	5.2
软件包管理器	Homebrew
软件包管理器页面	https://formulae.brew.sh/formula/cutadapt
主页	https://cutadapt.readthedocs.io
仓库	https://github.com/marcelm/cutadapt
上游文档	https://cutadapt.readthedocs.io/
许可证	MIT
源码归档	https://github.com/marcelm/cutadapt.git
最后更新	2026-05-04T20:29:09Z
Pulse	updated
依赖	python@3.14
Bottle	可用 (于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	未定义
服务	未声明

注册表事实

源数据库详情

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

源数据库匹配

其他软件包管理器记录

匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。

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 依赖
normalized package name match
匹配方式：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 依赖
normalized package name match
匹配方式：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

软件包图谱

链接来自本地软件包关系图、补充数据、依赖边、生态匹配和软件包 hub 归属。

来源线索

由仓库数据生成

此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。

Combined YAML source

View the package source record on GitHub.

combined/cutadapt.yml

使用的来源

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

使用 Homebrew, apt 安装 cutadapt