macOS
Homebrewverifiziert · 100%
brew install breseqlocal Homebrew formula metadata
brew / Rang 6416
breseq mit Homebrew, Nix installieren
Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für breseq in AI-Agent-Workflows.
Installation
Weitere Installationsbefehle
Linux
Nixverifiziert · 92%
nix profile install nixpkgs#breseqnixpkgs package indexes · pkgs/by-name/br/breseq/package.nix · Quelle: api.github.com
Überblick
Paketzusammenfassung
Computational pipeline for finding mutations in short-read DNA resequencing data
Projektlinks
Befehle und Aliase
- breseq
- gdtools
Verlauf
Projektgeschichte und Nutzung
breseq is a command-line microbial genomics pipeline for finding mutations in short-read resequencing data against a reference genome. It is associated with the Barrick Lab and is aimed especially at haploid microbial genomes, with companion tooling such as gdtools for working with GenomeDiff-style results.
Projektgeschichte
The project predates its 2015 GitHub import: its official citation file points users to a 2014 Methods in Molecular Biology article on identifying mutations in laboratory-evolved microbes with breseq, and to a 2014 BMC Genomics article on structural variation in haploid microbial genomes. The repository was created on GitHub in March 2015, with release v0.26.0 published shortly afterward.
breseq's documentation culture is unusually deep for a packaged CLI: the official wiki is a user manual with installation material, usage pages for breseq and gdtools, and tutorials for clones, populations, barcoded/targeted data, and curation workflows. The Barrick Lab homepage also links example output and tutorial data, reflecting its origin as a research-lab tool rather than a general developer utility.
Adoptionsgeschichte
Adoption is strongest in microbial evolution and resequencing workflows. Official project materials point users to GitHub releases and Bioconda, while Homebrew packages it for macOS and Linux users who want a system package. Homebrew analytics reported hundreds of installs over the prior year at lookup time, a niche but steady signal for a scientific command-line package.
Wie es verwendet wird
Users run breseq on short-read resequencing data to call mutations relative to a reference sequence, then use its HTML reports, GenomeDiff output, and gdtools utilities to inspect, compare, or curate results. The tool is especially relevant when experiments produce many evolved microbial clones or populations that need consistent mutation calling.
Warum Paket-Nerds sich dafür interessieren
For package nerds, breseq is a good example of research software that became a reproducible CLI package across multiple scientific distribution channels. It brings a citation-backed bioinformatics workflow, native C++ code, test data, tutorials, and platform packaging into the same ecosystem, which is exactly the kind of messy but valuable scientific tool package managers preserve.
Zeitleiste
- 2014: Preferred breseq methods article and related BMC Genomics article published.
- 2015: GitHub repository created and v0.26.0 release published.
- 2016-2017: 0.27 through 0.30 releases continued the public release series.
- 2024: v0.39.0 released.
- 2026: v0.40.1 released and Homebrew stable version reported as 0.40.1.
Related projects
- gdtools is shipped with breseq for GenomeDiff manipulation and downstream analysis.
- Bioconda distributes breseq for scientific package-management workflows, alongside Homebrew packaging for general Unix-like developer environments.
- The Barrick Lab tutorial data and example outputs are part of the practical ecosystem around the tool.
Quellen
Sicherheitslage
Risikostufe: grün
narrow executable package without higher-risk signals.
Risikoklassifikator
grün Risiko · niedrig Konfidenz · appliance
Warum
- narrow executable package without higher-risk signals
Signale
- metadata:no-higher-risk-signals
Installationsverhalten
- Es wurden keine Homebrew-Bottle-Metadaten erfasst.
Empfohlene Prüfung
Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.
Executables
Installierte Executables
| Befehl | Art | Sichtbarkeit | Hinweis |
|---|---|---|---|
breseq | Executable | indexiertes Executable | Aus dem lokalen Executable-Index erkannt. |
gdtools | Executable | indexiertes Executable | Aus dem lokalen Executable-Index erkannt. |
Aktualität
Version und Aktualität
Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.
Seite generiert2026-08-03
Manager-Version0.40.2
Manager aktualisiert2026-07-29
lokale Datenunbekannt
Upstreamnicht verfügbar
neueste erkannte Versionnicht erkannt
- OKEs wurden keine Aktualitätswarnungen generiert.
Installationsmetadaten
Paketmetadaten
| Paketschlüssel | brew:breseq |
|---|---|
| Version | 0.40.2 |
| Paketmanager | Homebrew |
| Homepage | https://barricklab.org/breseq |
| Repository | https://github.com/barricklab/breseq |
| Zuletzt aktualisiert | 2026-07-29T15:20:21Z |
| Pulse | updated |
| Bottle | nicht erfasst |
| Dienst | keiner deklariert |
Source-Datenbank-Treffer
Andere Paketmanager-Einträge
Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.
Nix95%
breseq
nix profile install nixpkgs#breseq- normalized package name match
- Abgeglichen nach: Breseq
Quellspur
Aus Repository-Daten generiert
Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.
Combined YAML source
View the package source record on GitHub.
Verwendete Quellen
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation