brew / rank 6749

Install flye with Homebrew, apt, Nix

De novo assembler for single molecule sequencing reads using repeat graphs. Version 2.9.6 via Homebrew; verified 2026-06-22. Also installable with debian: sudo apt install flye.

Install command Security notes

install

Additional install commands

macOS

Homebrewverified · 100%

brew install flye

local Homebrew formula metadata

Linux

Debian aptverified · 92%

sudo apt install flye

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

Nixverified · 92%

nix profile install nixpkgs#flye

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

overview

Package summary

De novo assembler for single molecule sequencing reads using repeat graphs

Project links

Homepage

Commands and aliases

flye
flye-minimap2
flye-modules
flye-samtools

history

Project history and usage

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.

Project history

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.

Adoption history

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.

How it is used

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.

Why package nerds care

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.

Timeline

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.

Sources

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

narrow executable package without higher-risk signals

Signals

metadata:no-higher-risk-signals

Install behavior

No Homebrew bottle metadata was recorded.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

Command	Kind	Exposure	Note
`flye`	executable	indexed executable	Discovered from the local executable index.
`flye-minimap2`	executable	indexed executable	Discovered from the local executable index.
`flye-modules`	executable	indexed executable	Discovered from the local executable index.
`flye-samtools`	executable	indexed executable	Discovered from the local executable index.

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-08-03

manager version2.9.6

manager updated2026-06-22

local dataunknown

upstreamnot available

latest detectednot detected

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:flye
Version	2.9.6
Package manager	Homebrew
Homepage	https://github.com/mikolmogorov/Flye
Repository	https://github.com/mikolmogorov/Flye
Last updated	2026-06-22T14:03:21-07:00
Pulse	updated
Bottle	not recorded
Service	none declared

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

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 dependencies
normalized package name match
Matched by: 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
Matched by: 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