# 使用 Homebrew, apt 安装 trim-galore 查看 trim-galore 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:trim-galore ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install trim-galore ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install trim-galore ``` 证据: Debian stable package indexes: trim-galore from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## 软件包事实 - **软件包键:** brew:trim-galore - **软件包管理器:** Homebrew - **版本:** 2.3.0 - **来源摘要:** Quality and adapter trimming for FastQ sequencing reads - **主页:** - **仓库:** - **最后更新:** 2026-07-11T13:10:09+02:00 - **已生成:** 2026-08-03T19:37:03+00:00 ## 可执行文件 - trim_galore (别名) ## 安装行为 - Bottle: 不可用 ## 版本和新鲜度 - 页面生成时间: 2026-08-03 - 管理器版本: 2.3.0 ## 项目历史与用法 Trim Galore is a command-line tool for adapter and quality trimming of FASTQ sequencing reads, with extra support for bisulfite and RRBS workflows. It began as a Perl wrapper around Cutadapt and FastQC and later moved to a Rust implementation that preserves the established command-line interface and output conventions. ### 项目历史 The original Trim Galore project was developed at Babraham Bioinformatics by Felix Krueger. Official Babraham documentation describes it as a wrapper around Cutadapt and FastQC for consistent quality and adapter trimming of FastQ files, including special handling for MspI-digested RRBS libraries. The official Trim Galore documentation describes v2.x as a faithful Rust rewrite of the earlier v0.6.x Perl tool. The rewrite consolidated adapter trimming, gzip handling, and FastQC-compatible reporting into a single static binary while retaining compatibility with common v0.6.x scripts and pipelines. ### 采用历史 Trim Galore became common in next-generation sequencing preprocessing because it wrapped the separate Cutadapt and FastQC steps behind one stable CLI and produced conventional FASTQ outputs plus trimming reports. The current docs describe more than ten years of production use and identify the older Perl wrapper as a de-facto standard in many bisulfite sequencing pipelines. Package-manager adoption spans bioinformatics and general Unix packaging channels: the supplied package facts list Homebrew, Debian, and Ubuntu package names, while the official installation guide documents Bioconda, crates.io, Docker, source builds, and prebuilt binaries as current installation paths. ### 使用方式 Typical usage is file-oriented and pipeline-friendly: run `trim_galore input.fastq.gz` for single-end reads, `trim_galore --paired sample_R1.fastq.gz sample_R2.fastq.gz` for paired-end reads, and add workflow-specific flags such as `--rrbs`, `--fastqc`, `--cores`, `--poly_a`, or explicit adapter specifications. Trim Galore writes trimmed FASTQ files and per-input trimming reports. The v2 documentation also describes structured JSON reports for MultiQC and an in-process FastQC-compatible reporting path. ### 为什么软件包爱好者会关心 Trim Galore matters to package-manager users because it sits at the boundary between classic scientific scripting and modern single-binary distribution. The old Perl-era package pulled together Perl, Python/Cutadapt, Java/FastQC, and compression tools; the v2 rewrite turns the same familiar CLI into a Rust binary with no runtime dependencies. For reproducible bioinformatics environments, it is notable that the official install page now supports multiple packaging cultures: Cargo/crates.io, Bioconda, Docker via GitHub Container Registry, source builds, and release binaries, while distro/package-manager metadata in the input shows Homebrew, Debian, and Ubuntu coverage. ### 时间线 - 2012: Official changelog lists v0.1.3 on 14 Mar 2012 and v0.1.4 on 21 Mar 2012. - 2013: v0.3.x releases expanded the early Perl wrapper line. - 2019: v0.6.0 was released on 1 Mar 2019. - 2021: v0.6.7 was released to obtain a Zenodo DOI. - 2026: v0.6.11 was released on 24 Feb 2026. - 2026: v2.x introduced the Rust rewrite as a single static binary and drop-in successor to v0.6.x. ### Related projects - Cutadapt was the adapter-trimming engine wrapped by the historical Perl Trim Galore implementation. - FastQC provided external quality-control reports in the older workflow; v2 integrates FastQC-compatible reporting through fastqc-rust. - MultiQC is relevant because Trim Galore reports, including v2 JSON reports, are intended for aggregation in sequencing QC workflows. ### 来源 - - - - - - - - source_facts.package-manager ## 安全说明 没有找到 trim-galore 的匹配本地密钥处理 manifest。Nucleus 软件包元数据仍在此发布，以便未来覆盖拥有稳定的软件包 URL。 ## 其他软件包管理器记录 - Debian apt - trim-galore - 0.6.10-1: normalized package name match | Debian stable package indexes: trim-galore from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | automate quality and adapter trimming for DNA sequencing | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ - Ubuntu apt - trim-galore - 0.6.10-1: normalized package name match | Ubuntu 24.04 LTS package indexes: trim-galore from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | automate quality and adapter trimming for DNA sequencing | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ## Combined YAML source View the package source record on GitHub. [combined/trim-galore.yml](https://github.com/mxcl/pkgdb/blob/main/combined/trim-galore.yml) ## 来源 - pkg.so package database - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph