macOS
Homebrewverified · 100%
brew install abysslocal Homebrew formula metadata
MacPortsverified · 94%
sudo port install abyssMacPorts ports tree · www/abyss/Portfile · source: api.github.com
brew / rank 5926
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
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install abyssDebian stable package indexes · abyss · source: deb.debian.org
overview
Package summary
Genome sequence assembler for short reads
Project links
Commands and aliases
- ABYSS
- ABYSS-P
- AdjList
- Consensus
- DAssembler
- DistanceEst
- DistanceEst-ssq
- KAligner
- MergeContigs
- MergePaths
- Overlap
- ParseAligns
- PathConsensus
- PathOverlap
- PopBubbles
- SimpleGraph
- abyss-align
- abyss-bloom
- abyss-bloom-dbg
- abyss-bloom-dist.mk
- abyss-bowtie
- abyss-bowtie2
- abyss-bwa
- abyss-bwamem
- abyss-bwasw
- abyss-db-csv
- abyss-db-txt
- abyss-dida
- abyss-fac
- abyss-fatoagp
- abyss-filtergraph
- abyss-fixmate
history
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
security posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
ABYSS | executable | indexed executable | Discovered from the local executable index. |
ABYSS-P | executable | indexed executable | Discovered from the local executable index. |
AdjList | executable | indexed executable | Discovered from the local executable index. |
Consensus | executable | indexed executable | Discovered from the local executable index. |
DAssembler | executable | indexed executable | Discovered from the local executable index. |
DistanceEst | executable | indexed executable | Discovered from the local executable index. |
DistanceEst-ssq | executable | indexed executable | Discovered from the local executable index. |
KAligner | executable | indexed executable | Discovered from the local executable index. |
MergeContigs | executable | indexed executable | Discovered from the local executable index. |
MergePaths | executable | indexed executable | Discovered from the local executable index. |
Overlap | executable | indexed executable | Discovered from the local executable index. |
ParseAligns | executable | indexed executable | Discovered from the local executable index. |
PathConsensus | executable | indexed executable | Discovered from the local executable index. |
PathOverlap | executable | indexed executable | Discovered from the local executable index. |
PopBubbles | executable | indexed executable | Discovered from the local executable index. |
SimpleGraph | executable | indexed executable | Discovered from the local executable index. |
abyss-align | executable | indexed executable | Discovered from the local executable index. |
abyss-bloom | executable | indexed executable | Discovered from the local executable index. |
abyss-bloom-dbg | executable | indexed executable | Discovered from the local executable index. |
abyss-bloom-dist.mk | executable | indexed executable | Discovered from the local executable index. |
abyss-bowtie | executable | indexed executable | Discovered from the local executable index. |
abyss-bowtie2 | executable | indexed executable | Discovered from the local executable index. |
abyss-bwa | executable | indexed executable | Discovered from the local executable index. |
abyss-bwamem | executable | indexed executable | Discovered from the local executable index. |
abyss-bwasw | executable | indexed executable | Discovered from the local executable index. |
abyss-db-csv | executable | indexed executable | Discovered from the local executable index. |
abyss-db-txt | executable | indexed executable | Discovered from the local executable index. |
abyss-dida | executable | indexed executable | Discovered from the local executable index. |
abyss-fac | executable | indexed executable | Discovered from the local executable index. |
abyss-fatoagp | executable | indexed executable | Discovered from the local executable index. |
abyss-filtergraph | executable | indexed executable | Discovered from the local executable index. |
abyss-fixmate | executable | indexed executable | Discovered from the local executable index. |
abyss-fixmate-ssq | executable | indexed executable | Discovered from the local executable index. |
abyss-gapfill | executable | indexed executable | Discovered from the local executable index. |
abyss-gc | executable | indexed executable | Discovered from the local executable index. |
abyss-index | executable | indexed executable | Discovered from the local executable index. |
abyss-junction | executable | indexed executable | Discovered from the local executable index. |
abyss-kaligner | executable | indexed executable | Discovered from the local executable index. |
abyss-layout | executable | indexed executable | Discovered from the local executable index. |
abyss-longseqdist | executable | indexed executable | Discovered from the local executable index. |
abyss-map | executable | indexed executable | Discovered from the local executable index. |
abyss-map-ssq | executable | indexed executable | Discovered from the local executable index. |
abyss-mergepairs | executable | indexed executable | Discovered from the local executable index. |
abyss-overlap | executable | indexed executable | Discovered from the local executable index. |
abyss-paired-dbg | executable | indexed executable | Discovered from the local executable index. |
abyss-paired-dbg-mpi | executable | indexed executable | Discovered from the local executable index. |
abyss-pe | executable | indexed executable | Discovered from the local executable index. |
abyss-rresolver-short | executable | indexed executable | Discovered from the local executable index. |
abyss-samtoafg | executable | indexed executable | Discovered from the local executable index. |
abyss-scaffold | executable | indexed executable | Discovered from the local executable index. |
abyss-sealer | executable | indexed executable | Discovered from the local executable index. |
abyss-stack-size | executable | indexed executable | Discovered from the local executable index. |
abyss-tabtomd | executable | indexed executable | Discovered from the local executable index. |
abyss-todot | executable | indexed executable | Discovered from the local executable index. |
abyss-tofastq | executable | indexed executable | Discovered from the local executable index. |
konnector | executable | indexed executable | Discovered from the local executable index. |
logcounter | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version2.3.10
manager updated2026-07-04
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:abyss |
|---|---|
| Version | 2.3.10 |
| Package manager | Homebrew |
| Homepage | https://www.bcgsc.ca/resources/software/abyss |
| Repository | https://github.com/BirolLab/abyss |
| Last updated | 2026-07-04T16:53:41+09:00 |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
abyss 2.3.10-1+b1
de novo, parallel, sequence assembler for short reads
https://github.com/bcgsc/abyss
sudo apt install abyss- Section: science
- Architecture: amd64
- Source Package: abyss
- 11 dependencies
- normalized package name match
- Matched by: Abyss
Ubuntu apt95%
abyss 2.3.7-2ubuntu3
de novo, parallel, sequence assembler for short reads
https://github.com/bcgsc/abyss
sudo apt install abyss- Section: universe/science
- Architecture: amd64
- 11 dependencies
- normalized package name match
- Matched by: Abyss
MacPorts95%
abyss
sudo port install abyss- normalized package name match
- Matched by: Abyss
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation