Installation

Weitere Installationsbefehle

macOS

Homebrewverifiziert · 100%

brew install flye

local Homebrew formula metadata

Linux

Debian aptverifiziert · 92%

sudo apt install flye

Debian stable package indexes · flye · Quelle: deb.debian.org

Nixverifiziert · 92%

nix profile install nixpkgs#flye

nixpkgs package indexes · pkgs/by-name/fl/flye/package.nix · Quelle: api.github.com

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

In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
Installiert mit 2 Laufzeitabhängigkeiten.

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
`flye`	cli	globales Executable
`flye-minimap2`	cli	globales Executable
`flye-modules`	cli	globales Executable
`flye-samtools`	cli	globales Executable

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 generiert2026-07-10

Manager-Version2.9.6

Manager aktualisiert2026-06-22

lokale DatenOK

Upstreamaktuell

neueste erkannte Version2.9.6

https://github.com/mikolmogorov/Flye

OKEs wurden keine Aktualitätswarnungen generiert.

Installationsmetadaten

Paketmetadaten

Paketschlüssel	brew:flye
Version	2.9.6
Paketmanager	Homebrew
Paketmanager-Seite	https://formulae.brew.sh/formula/flye
Homepage	https://github.com/mikolmogorov/Flye
Repository	https://github.com/mikolmogorov/Flye
Upstream-Dokumentation	https://github.com/mikolmogorov/Flye
Lizenz	BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT
Quellarchiv	https://github.com/mikolmogorov/Flye/archive/refs/tags/2.9.6.tar.gz
Zuletzt aktualisiert	2026-06-22T14:03:21-07:00
Pulse	updated
Abhängigkeiten	python@3.14, samtools
Bottle	verfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	nicht definiert
Dienst	keiner deklariert

Registry-Fakten

Details aus der Quelldatenbank

Source Database	Homebrew formula API
Tap	homebrew/core
Full Name	flye
Version Scheme	0
Revision	0
Head Version	HEAD
Bottle Stable Root URL	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	head stable

Source-Datenbank-Treffer

Andere Paketmanager-Einträge

Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.

Debian apt95%

flye 2.9.5+dfsg-1

de novo assembler for single molecule sequencing reads using repeat graphs

https://github.com/fenderglass/Flye

sudo apt install flye

Section: science
Architecture: amd64
8 Abhängigkeiten
normalized package name match
Abgeglichen nach: Flye

Debian stable package indexes · deb.debian.org · Debian stable package indexes: flye from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Nix95%

flye

nix profile install nixpkgs#flye

normalized package name match
Abgeglichen nach: Flye

nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/fl/flye/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

Ubuntu apt95%

flye 2.9.3+dfsg2-1

de novo assembler for single molecule sequencing reads using repeat graphs

https://github.com/fenderglass/Flye

sudo apt install flye

Section: universe/science
Architecture: amd64
8 Abhängigkeiten
normalized package name match
Abgeglichen nach: Flye

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: flye from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

Paketgraph

Links stammen aus dem lokalen Paketbeziehungsgraph, Ergänzungen, Abhängigkeitskanten, Ecosystem-Matches und Paket-Hub-Mitgliedschaft.

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.

combined/flye.yml

Verwendete Quellen

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

flye mit Homebrew, apt, Nix installieren