使用 Homebrew 安装 abricate

项目链接

• 主页

命令和别名

• abricate
• abricate-get_db

项目历史

The first GitHub release, v0.1, was published as 'Debut' on April 2, 2015. The README describes the project as mass screening of contigs for antimicrobial resistance or virulence genes and explains that the name combines the common acronym ABR, for antibiotic resistance, with an English-verb-like form.

采用历史

ABRicate became useful in workflow packaging because the README documents Bioconda installation, source installation, dependency checks, database setup, and operation through a single abricate command. The current Homebrew input metadata shows it packaged for Homebrew, while upstream also advertises Bioconda download badges.

使用方式

The tool screens assemblies, not raw FASTQ reads, and reports gene hits with coverage, identity, database, accession, product, and resistance fields. It can process many files, read a file-of-filenames, summarize reports into a presence/absence matrix, update bundled databases, and build custom nucleotide databases.

为什么软件包爱好者会关心

ABRicate is a classic bioinformatics packaging target: a Perl entry point with external command dependencies, bundled or downloadable reference databases, and a check/setup workflow that packagers and workflow engines can exercise after install. Its release history also tracks database refreshes and CI migration.

时间线

• 2015: v0.1 Debut release.
• 2020: v1.0.0 added file-of-filenames scanning, defaults around coverage/identity thresholds, MEGARES docs, and NCBI/CARD database support.
• 2025: v1.2.0 refreshed databases, moved CI to GitHub Actions, switched download code to Perl File::Fetch, and improved docs.
• 2026: v1.4.0 added a UPEC/ExPEC virulence-factors database and updated NCBI AMR data.

Related projects

• The README points users to ARIBA, ResFinder, RGI, SRST2, and AMRFinderPlus when ABRicate is not the right fit. It also bundles or references databases including NCBI AMRFinderPlus, CARD, ResFinder, ARG-ANNOT, MEGARES, PlasmidFinder, VFDB, VICTORS, BacMet, and UPEC/ExPEC VF.

来源

• https://github.com/tseemann/abricate#readme
• https://github.com/tseemann/abricate/releases
• input source_facts.package-manager