# Install abyss with Homebrew, apt, MacPorts

Genome sequence assembler for short reads. Version 2.3.10 via Homebrew; verified 2026-07-04. Also installable with debian: sudo apt install abyss.

## Install

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

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install abyss
```

  Evidence: local Homebrew formula metadata

- MacPorts (94%):

```sh
sudo port install abyss
```

  Evidence: 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
```

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

## Package facts

- **Package key:** brew:abyss
- **Package manager:** Homebrew
- **Version:** 2.3.10
- **Source summary:** Genome sequence assembler for short reads
- **Homepage:** <https://www.bcgsc.ca/resources/software/abyss>
- **Repository:** <https://github.com/BirolLab/abyss>
- **Last updated:** 2026-07-04T16:53:41+09:00
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

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

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 2.3.10
## Project history and usage

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.

### Project history

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.

### Adoption history

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.

### How it is used

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.

### Why package nerds care

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.

### Timeline

- 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.

### Sources

- <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


## 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 - 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


## Combined YAML source

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