# abyss を Homebrew, apt, MacPorts でインストール

abyss のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

## インストール

```sh
sudo av install brew:abyss
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install abyss
```

  証拠: local Homebrew formula metadata

- MacPorts (94%):

```sh
sudo port install abyss
```

  証拠: MacPorts ports tree: www/abyss/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

### Linux

- Debian apt (92%):

```sh
sudo apt install abyss
```

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

## パッケージ情報

- **パッケージキー:** brew:abyss
- **パッケージマネージャ:** Homebrew
- **パッケージマネージャページ:** <https://formulae.brew.sh/formula/abyss>
- **バージョン:** 2.3.10
- **ソース概要:** Genome sequence assembler for short reads
- **ホームページ:** <https://www.bcgsc.ca/resources/software/abyss>
- **リポジトリ:** <https://github.com/BirolLab/abyss>
- **上流ドキュメント:** <https://github.com/bcgsc/abyss#readme>
- **ライセンス:** GPL-3.0-only AND LGPL-2.1-or-later AND MIT AND BSD-3-Clause
- **ソースアーカイブ:** <https://github.com/BirolLab/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz>
- **最終更新:** 2026-07-04T16:53:41+09:00
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- ABYSS (cli)
- ABYSS-P (cli)
- AdjList (cli)
- Consensus (cli)
- DAssembler (cli)
- DistanceEst (cli)
- DistanceEst-ssq (cli)
- KAligner (cli)
- MergeContigs (cli)
- MergePaths (cli)
- Overlap (cli)
- ParseAligns (cli)
- PathConsensus (cli)
- PathOverlap (cli)
- PopBubbles (cli)
- SimpleGraph (cli)
- abyss-align (cli)
- abyss-bloom (cli)
- abyss-bloom-dbg (cli)
- abyss-bloom-dist.mk (cli)
- abyss-bowtie (cli)
- abyss-bowtie2 (cli)
- abyss-bwa (cli)
- abyss-bwamem (cli)
- abyss-bwasw (cli)
- abyss-db-csv (cli)
- abyss-db-txt (cli)
- abyss-dida (cli)
- abyss-fac (cli)
- abyss-fatoagp (cli)
- abyss-filtergraph (cli)
- abyss-fixmate (cli)
- abyss-fixmate-ssq (cli)
- abyss-gapfill (cli)
- abyss-gc (cli)
- abyss-index (cli)
- abyss-junction (cli)
- abyss-kaligner (cli)
- abyss-layout (cli)
- abyss-longseqdist (cli)
- abyss-map (cli)
- abyss-map-ssq (cli)
- abyss-mergepairs (cli)
- abyss-overlap (cli)
- abyss-paired-dbg (cli)
- abyss-paired-dbg-mpi (cli)
- abyss-pe (cli)
- abyss-rresolver-short (cli)
- abyss-samtoafg (cli)
- abyss-scaffold (cli)
- abyss-sealer (cli)
- abyss-stack-size (cli)
- abyss-tabtomd (cli)
- abyss-todot (cli)
- abyss-tofastq (cli)
- konnector (cli)
- logcounter (cli)
- ABYSS (エイリアス)
- ABYSS-P (エイリアス)
- AdjList (エイリアス)
- Consensus (エイリアス)
- DAssembler (エイリアス)
- DistanceEst (エイリアス)
- DistanceEst-ssq (エイリアス)
- KAligner (エイリアス)
- MergeContigs (エイリアス)
- MergePaths (エイリアス)
- Overlap (エイリアス)
- ParseAligns (エイリアス)
- PathConsensus (エイリアス)
- PathOverlap (エイリアス)
- PopBubbles (エイリアス)
- SimpleGraph (エイリアス)
- abyss-align (エイリアス)
- abyss-bloom (エイリアス)
- abyss-bloom-dbg (エイリアス)
- abyss-bloom-dist.mk (エイリアス)
- abyss-bowtie (エイリアス)
- abyss-bowtie2 (エイリアス)
- abyss-bwa (エイリアス)
- abyss-bwamem (エイリアス)
- abyss-bwasw (エイリアス)
- abyss-db-csv (エイリアス)
- abyss-db-txt (エイリアス)
- abyss-dida (エイリアス)
- abyss-fac (エイリアス)
- abyss-fatoagp (エイリアス)
- abyss-filtergraph (エイリアス)
- abyss-fixmate (エイリアス)
- abyss-fixmate-ssq (エイリアス)
- abyss-gapfill (エイリアス)
- abyss-gc (エイリアス)
- abyss-index (エイリアス)
- abyss-junction (エイリアス)
- abyss-kaligner (エイリアス)
- abyss-layout (エイリアス)
- abyss-longseqdist (エイリアス)
- abyss-map (エイリアス)
- abyss-map-ssq (エイリアス)
- abyss-mergepairs (エイリアス)
- abyss-overlap (エイリアス)
- abyss-paired-dbg (エイリアス)
- abyss-paired-dbg-mpi (エイリアス)
- abyss-pe (エイリアス)
- abyss-rresolver-short (エイリアス)
- abyss-samtoafg (エイリアス)
- abyss-scaffold (エイリアス)
- abyss-sealer (エイリアス)
- abyss-stack-size (エイリアス)
- abyss-tabtomd (エイリアス)
- abyss-todot (エイリアス)
- abyss-tofastq (エイリアス)
- konnector (エイリアス)
- logcounter (エイリアス)

## 依存関係

- btllib
- libomp
- open-mpi

## ビルド依存関係

- boost
- google-sparsehash

## macOS 提供ライブラリ

- sqlite

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-07-08
- マネージャ版: 2.3.10
- マネージャ更新日: 2026-07-04
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/BirolLab/abyss
- 情報: No cached GitHub release or tag data was available.
## プロジェクトの歴史と使われ方

ABySS is a de novo genome sequence assembler for short paired-end reads, developed at the BC Cancer Genome Sciences Centre and distributed as command-line tools such as abyss-pe and ABYSS-P.

### プロジェクトの歴史

The official changelog records ABySS 1.0 on 2008-08-07. Its 2009 Genome Research paper described ABySS as a parallel assembler for short-read sequence data, and the project page identifies it as a parallel, paired-end assembler using MPI for larger genomes.

ABySS 2.0, released in 2016 and described in a 2017 Genome Research paper, added a Bloom filter assembly mode to reduce memory use for large genomes. Later releases continued to tune Bloom filter assembly, linked-read scaffolding, RResolver integration, and compiler/platform support.

### 採用の歴史

ABySS became part of bioinformatics packaging culture because it exposed a substantial Unix-style command suite around a reproducible assembly pipeline and was packaged by Homebrew, Debian, Ubuntu, MacPorts, and Bioconda.

The project page notes a 2015 International Bioinformatics Resource Award from the Swiss Institute of Bioinformatics, reflecting broader scientific use beyond the original BC Cancer group.

### 使われ方

Typical use is batch-oriented: users install ABySS through Conda, Homebrew, or from source, then run abyss-pe with parameters such as k and Bloom filter memory settings for paired-end short-read assembly.

The README documents cluster-oriented MPI mode, Bloom filter mode, scaffolding, linked-read workflows, and related tools such as ARCS, Tigmint, Konnector, Sealer, and abyss-bloom.

### パッケージ好きにとっての重要性

ABySS matters to package maintainers because it combines compiled C++ code, MPI/OpenMP, optional scientific dependencies, many installed executables, and large-memory workloads in one formula.

It is a good example of a scientific CLI whose packaging value is not just the top-level binary but a coordinated toolchain used inside reproducible bioinformatics pipelines.

### タイムライン

- 2008: ABySS 1.0 released.
- 2009: Genome Research paper presents ABySS as a parallel assembler for short-read sequence data.
- 2015: ABySS wins the Swiss Institute of Bioinformatics International Bioinformatics Resource Award.
- 2016: ABySS 2.0 introduces Bloom filter assembly mode.
- 2017: ABySS 2.0 paper describes resource-efficient large-genome assembly using a Bloom filter.
- 2021: ABySS 2.3.0 makes RResolver part of the default pipeline.

### Related projects

- Related projects in the official README include Trans-ABySS, ARCS, Tigmint, Konnector, Sealer, btllib, Open MPI, Boost, and samtools.

### ソース

- <https://github.com/bcgsc/abyss#readme>
- <https://raw.githubusercontent.com/bcgsc/abyss/master/ChangeLog>
- <https://www.bcgsc.ca/resources/software/abyss>
- source_facts.package-manager


## セキュリティノート

narrow executable package without higher-risk signals.

- **Geiger リスク:** グリーン / 低
- narrow executable package without higher-risk signals

## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** abyss
- **Version Scheme:** 0
- **Revision:** 1
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable

## 他のパッケージマネージャ記録

- Debian apt - abyss - 2.3.10-1+b1: normalized package name match | Debian stable package indexes: abyss from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | de novo, parallel, sequence assembler for short reads | https://github.com/bcgsc/abyss
- Ubuntu apt - abyss - 2.3.7-2ubuntu3: normalized package name match | Ubuntu 24.04 LTS package indexes: abyss from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | de novo, parallel, sequence assembler for short reads | https://github.com/bcgsc/abyss
- MacPorts - abyss: normalized package name match | MacPorts ports tree: www/abyss/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1


## 関連リンク

- [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [Homebrew utility packages](https://www.automicvault.com/ja/pkg/brew-utility-packages/) - Matched Homebrew package provider.
- [btllib](https://www.automicvault.com/ja/pkg/brew/btllib/) - Runtime dependency declared by Homebrew.
- [open-mpi](https://www.automicvault.com/ja/pkg/brew/open-mpi/) - Runtime dependency declared by Homebrew.
- [flye](https://www.automicvault.com/ja/pkg/brew/flye/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
- [spades](https://www.automicvault.com/ja/pkg/brew/spades/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
- [polypolish](https://www.automicvault.com/ja/pkg/brew/polypolish/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science, short-reads.
- [bwa](https://www.automicvault.com/ja/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, science, short-reads.
- [abpoa](https://www.automicvault.com/ja/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [abricate](https://www.automicvault.com/ja/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [adapterremoval](https://www.automicvault.com/ja/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [alevin-fry](https://www.automicvault.com/ja/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/abyss.yml](https://github.com/automic-vault/db/blob/main/combined/abyss.yml)


## ソース

- 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