# 使用 Homebrew, apt, Nix 安装 flye

查看 flye 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。

## 安装

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

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install flye
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install flye
```

  证据: 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
```

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

## 软件包事实

- **软件包键:** brew:flye
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/flye>
- **版本:** 2.9.6
- **来源摘要:** De novo assembler for single molecule sequencing reads using repeat graphs
- **主页:** <https://github.com/mikolmogorov/Flye>
- **仓库:** <https://github.com/mikolmogorov/Flye>
- **许可证:** BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT
- **源码归档:** <https://github.com/mikolmogorov/Flye/archive/refs/tags/2.9.6.tar.gz>
- **最后更新:** 2026-06-22T14:03:21-07:00
- **已生成:** 2026-08-04T22:13:35+00:00

## 可执行文件

- flye (cli)
- flye-minimap2 (cli)
- flye-modules (cli)
- flye-samtools (cli)
- flye (别名)
- flye-minimap2 (别名)
- flye-modules (别名)
- flye-samtools (别名)

## 依赖

- python@3.14
- samtools

## 安装行为

- post-install 钩子: 未定义
- Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## 版本和新鲜度

- 页面生成时间: 2026-08-04
- 管理器版本: 2.9.6
- 管理器更新时间: 2026-06-22
- 本地数据: OK
- 上游仓库: https://github.com/mikolmogorov/Flye
- 检测到的最新版本: 2.9.6 (当前)
## 项目历史与用法

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.

### 项目历史

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.

### 采用历史

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.

### 使用方式

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.

### 为什么软件包爱好者会关心

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.

### 时间线

- 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.

### 来源

- <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>


## 安全说明

narrow executable package without higher-risk signals.

- **Geiger 风险:** 绿色 / 低
- narrow executable package without higher-risk signals

## 源数据库详情

- **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

## 其他软件包管理器记录

- 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


## 相关链接

- [Source-control packages](https://pkg.so/zh-hans/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://pkg.so/zh-hans/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://pkg.so/zh-hans/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://pkg.so/zh-hans/scientific-computing-tools/) - Matched scientific computing metadata.
- [python@3.14](https://pkg.so/zh-hans/brew/python-3-14/) - Runtime dependency declared by Homebrew.
- [samtools](https://pkg.so/zh-hans/brew/samtools/) - Runtime dependency declared by Homebrew.
- [spades](https://pkg.so/zh-hans/brew/spades/) - Shares pkgdb curated category or tags: bioinformatics, cli, genome-assembly, science.
- [abyss](https://pkg.so/zh-hans/brew/abyss/) - Shares pkgdb curated category or tags: bioinformatics, cli, genome-assembly, science.
- [autocycler](https://pkg.so/zh-hans/brew/autocycler/) - Shares pkgdb curated category or tags: bioinformatics, cli, long-read-sequencing, science.
- [polypolish](https://pkg.so/zh-hans/brew/polypolish/) - Shares pkgdb curated category or tags: bioinformatics, cli, genome-assembly, science.
- [oarfish](https://pkg.so/zh-hans/brew/oarfish/) - Shares pkgdb curated category or tags: bioinformatics, cli, long-read-sequencing, science.
- [chopper](https://pkg.so/zh-hans/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, long-read-sequencing, science.
- [nanoq](https://pkg.so/zh-hans/brew/nanoq/) - Shares pkgdb curated category or tags: bioinformatics, cli, nanopore, science.
- [badread](https://pkg.so/zh-hans/brew/badread/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, long, python, python-3-14.

## Combined YAML source

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


## 来源

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