# 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. ## 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 - **Package manager page:** - **Version:** 2.9.6 - **Source summary:** De novo assembler for single molecule sequencing reads using repeat graphs - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT - **Source archive:** - **Last updated:** 2026-06-22T14:03:21-07:00 - **Generated:** 2026-07-08T18:08:21+00:00 ## Executables - flye (cli) - flye-minimap2 (cli) - flye-modules (cli) - flye-samtools (cli) - flye (alias) - flye-minimap2 (alias) - flye-modules (alias) - flye-samtools (alias) ## Dependencies - python@3.14 - samtools ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 2.9.6 - Package-manager updated: 2026-06-22 - Local data: ok - Upstream repository: https://github.com/mikolmogorov/Flye - Upstream latest detected: 2.9.6 (current) ## 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 Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## 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:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 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 ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [python@3.14](https://www.automicvault.com/pkg/brew/python-3-14/) - Runtime dependency declared by Homebrew. - [samtools](https://www.automicvault.com/pkg/brew/samtools/) - Runtime dependency declared by Homebrew. - [abyss](https://www.automicvault.com/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science. - [spades](https://www.automicvault.com/pkg/brew/spades/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science. - [oarfish](https://www.automicvault.com/pkg/brew/oarfish/) - Shares av.db curated category or tags: bioinformatics, cli, long-read-sequencing, science. - [polypolish](https://www.automicvault.com/pkg/brew/polypolish/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science. - [abpoa](https://www.automicvault.com/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science. ## Combined YAML source View the package source record on GitHub. [combined/flye.yml](https://github.com/automic-vault/db/blob/main/combined/flye.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph