macOS
Homebrewverifiziert · 100%
brew install flyeprovider-native install command
brew / Rang 6736
flye mit Homebrew installieren
Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für flye in AI-Agent-Workflows.
Installation
Weitere Installationsbefehle
Überblick
Paketzusammenfassung
De novo assembler for single molecule sequencing reads using repeat graphs
Projektlinks
Befehle und Aliase
- flye
- flye-minimap2
- flye-modules
- flye-samtools
Verlauf
Projektgeschichte und Nutzung
Flye is a de novo assembler for long, single-molecule sequencing reads from platforms such as PacBio and Oxford Nanopore. It is distributed as a command-line bioinformatics package and presents a complete assembly pipeline from raw reads to polished contigs, with special support for metagenome assembly through metaFlye.
Projektgeschichte
The project grew out of the ABruijn/Flye line of assemblers developed in Pavel Pevzner's lab at UCSD. Its official release history shows early releases under the ABruijn name in 2016 and 2017, followed by Flye releases from the 2.x series onward.
Flye's core technical identity is its repeat graph approach. The README describes repeat graphs as an alternative to de Bruijn graphs for noisy long-read data, using approximate sequence matches and classifying graph edges as unique or repetitive to support reconstruction of assemblies.
Adoptionsgeschichte
Flye became a standard packaged long-read assembler in bioinformatics workflows because it targets both PacBio and Oxford Nanopore reads, covers bacterial through mammalian-scale assemblies, and advertises Bioconda installation from the official README. The input package metadata also records packaging across Homebrew, Debian, Ubuntu, and Nix.
Wie es verwendet wird
Typical usage is as the `flye` CLI: users provide raw PacBio or ONT reads, select the appropriate read mode, and receive polished contigs and graph outputs. The README also documents metagenome assembly, benchmark datasets, and downstream visualization or phasing tools.
Warum Paket-Nerds sich dafür interessieren
Flye is notable to package maintainers because it combines Python/C++ bioinformatics code with bundled third-party components such as minimap2 and samtools, while remaining a user-facing CLI. It is also a good example of a research tool that crossed into routine package-manager distribution because long-read sequencing became common laboratory infrastructure.
Zeitleiste
- 2016: ABruijn v1.0 was released.
- 2018: The 2.3 release line appeared under the Flye name.
- 2019: The Flye repeat-graph assembler paper was published in Nature Biotechnology.
- 2020: metaFlye for long-read metagenome assembly was published in Nature Methods.
- 2021: Flye 2.9 added updated high-quality Nanopore and HiFi behavior and other assembly improvements.
- 2025: Flye 2.9.6 was released as a minor fix release.
Related projects
- Related projects named by the official README include metaFlye, HapDup, strainy, AGB, Bandage, minimap2, and samtools.
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 |
|---|---|---|---|
flye | Executable | indexiertes Executable | Aus dem lokalen Executable-Index erkannt. |
flye-minimap2 | Executable | indexiertes Executable | Aus dem lokalen Executable-Index erkannt. |
flye-modules | Executable | indexiertes Executable | Aus dem lokalen Executable-Index erkannt. |
flye-samtools | 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-Version2.9.6
Manager aktualisiert2026-06-22
lokale Datenunbekannt
Upstreamnicht verfügbar
neueste erkannte Versionnicht erkannt
- OKEs wurden keine Aktualitätswarnungen generiert.
Installationsmetadaten
Paketmetadaten
| Paketschlüssel | brew:flye |
|---|---|
| Version | 2.9.6 |
| Paketmanager | Homebrew |
| Homepage | https://github.com/mikolmogorov/Flye |
| Repository | https://github.com/mikolmogorov/Flye |
| Zuletzt aktualisiert | 2026-06-22T14:03:21-07:00 |
| Pulse | updated |
| Bottle | nicht erfasst |
| Dienst | keiner deklariert |
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
- Nucleus package database
- curated package history
- pkgdb category and tag curation