# 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

```sh
sudo av install brew:flye
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install flye
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install flye
```

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

- Nix (92%):

```sh
nix profile install nixpkgs#flye
```

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

## Package facts

- **Package key:** brew:flye
- **Package manager:** Homebrew
- **Version:** 2.9.6
- **Source summary:** De novo assembler for single molecule sequencing reads using repeat graphs
- **Homepage:** <https://github.com/mikolmogorov/Flye>
- **Repository:** <https://github.com/mikolmogorov/Flye>
- **Last updated:** 2026-06-22T14:03:21-07:00
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- flye (alias)
- flye-minimap2 (alias)
- flye-modules (alias)
- flye-samtools (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 2.9.6
## 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

- <https://api.github.com/repos/mikolmogorov/Flye/releases?per_page=100>
- <https://github.com/mikolmogorov/Flye>
- <https://raw.githubusercontent.com/mikolmogorov/Flye/flye/README.md>


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Other Package-Manager Records

- Debian apt - flye - 2.9.5+dfsg-1: normalized package name match | Debian stable package indexes: flye from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | de novo assembler for single molecule sequencing reads using repeat graphs | https://github.com/fenderglass/Flye
- Nix - flye: normalized package name match | nixpkgs package indexes: pkgs/by-name/fl/flye/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - flye - 2.9.3+dfsg2-1: normalized package name match | Ubuntu 24.04 LTS package indexes: flye from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | de novo assembler for single molecule sequencing reads using repeat graphs | https://github.com/fenderglass/Flye


## Combined YAML source

View the package source record on GitHub. [combined/flye.yml](https://github.com/mxcl/pkgdb/blob/main/combined/flye.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph