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

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 post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 2 runtime dependencies.

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
`flye`	cli	global executable
`flye-minimap2`	cli	global executable
`flye-modules`	cli	global executable
`flye-samtools`	cli	global executable

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 generated2026-07-08

manager version2.9.6

manager updated2026-06-22

local dataok

upstreamcurrent

latest detected2.9.6

https://github.com/mikolmogorov/Flye

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:flye
Version	2.9.6
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/flye
Homepage	https://github.com/mikolmogorov/Flye
Repository	https://github.com/mikolmogorov/Flye
Upstream docs	https://github.com/mikolmogorov/Flye
License	BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT
Source archive	https://github.com/mikolmogorov/Flye/archive/refs/tags/2.9.6.tar.gz
Last updated	2026-06-22T14:03:21-07:00
Pulse	updated
Dependencies	python@3.14, samtools
Bottle	available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	not defined
Service	none declared

registry facts

Source database details

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 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

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 dependencies
normalized package name match
Matched by: 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

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Combined YAML source

View the package source record on GitHub.

combined/flye.yml

Used sources

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

Install flye with Homebrew, apt, Nix