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brew

Install abyss with Homebrew, apt, MacPorts

Genome sequence assembler for short reads. Version 2.3.10 via Homebrew; verified 2026-07-04.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install abyss

local Homebrew formula metadata

MacPortsverified · 94%
sudo port install abyss

MacPorts ports tree · www/abyss/Portfile · source: api.github.com

Linux

Debian aptverified · 92%
sudo apt install abyss

Debian stable package indexes · abyss · source: deb.debian.org

overview

Package summary

Genome sequence assembler for short reads

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.

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 post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 3 runtime dependencies.
  • Build metadata lists 2 build dependencies.

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

CommandKindExposureNote
ABYSScliglobal executable
ABYSS-Pcliglobal executable
AdjListcliglobal executable
Consensuscliglobal executable
DAssemblercliglobal executable
DistanceEstcliglobal executable
DistanceEst-ssqcliglobal executable
KAlignercliglobal executable
MergeContigscliglobal executable
MergePathscliglobal executable
Overlapcliglobal executable
ParseAlignscliglobal executable
PathConsensuscliglobal executable
PathOverlapcliglobal executable
PopBubblescliglobal executable
SimpleGraphcliglobal executable
abyss-aligncliglobal executable
abyss-bloomcliglobal executable
abyss-bloom-dbgcliglobal executable
abyss-bloom-dist.mkcliglobal executable
abyss-bowtiecliglobal executable
abyss-bowtie2cliglobal executable
abyss-bwacliglobal executable
abyss-bwamemcliglobal executable
abyss-bwaswcliglobal executable
abyss-db-csvcliglobal executable
abyss-db-txtcliglobal executable
abyss-didacliglobal executable
abyss-faccliglobal executable
abyss-fatoagpcliglobal executable
abyss-filtergraphcliglobal executable
abyss-fixmatecliglobal executable
abyss-fixmate-ssqcliglobal executable
abyss-gapfillcliglobal executable
abyss-gccliglobal executable
abyss-indexcliglobal executable
abyss-junctioncliglobal executable
abyss-kalignercliglobal executable
abyss-layoutcliglobal executable
abyss-longseqdistcliglobal executable
abyss-mapcliglobal executable
abyss-map-ssqcliglobal executable
abyss-mergepairscliglobal executable
abyss-overlapcliglobal executable
abyss-paired-dbgcliglobal executable
abyss-paired-dbg-mpicliglobal executable
abyss-pecliglobal executable
abyss-rresolver-shortcliglobal executable
abyss-samtoafgcliglobal executable
abyss-scaffoldcliglobal executable
abyss-sealercliglobal executable
abyss-stack-sizecliglobal executable
abyss-tabtomdcliglobal executable
abyss-todotcliglobal executable
abyss-tofastqcliglobal executable
konnectorcliglobal executable
logcountercliglobal executable

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 generated2026-07-08
manager version2.3.10
manager updated2026-07-04
local dataok
upstreamnot checked
latest detectednot detected

https://github.com/BirolLab/abyss

install metadata

Package metadata

Package keybrew:abyss
Version2.3.10
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/abyss
Homepagehttps://www.bcgsc.ca/resources/software/abyss
Repositoryhttps://github.com/BirolLab/abyss
Upstream docshttps://github.com/bcgsc/abyss#readme
LicenseGPL-3.0-only AND LGPL-2.1-or-later AND MIT AND BSD-3-Clause
Source archivehttps://github.com/BirolLab/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz
Last updated2026-07-04T16:53:41+09:00
Pulseupdated
Dependenciesbtllib, libomp, open-mpi
Build dependenciesboost, google-sparsehash
Uses from macOSsqlite
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Nameabyss
Version Scheme0
Revision1
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

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
Debian stable package indexes · deb.debian.org · Debian stable package indexes: abyss from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: abyss from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
MacPorts95%

abyss

sudo port install abyss
  • normalized package name match
  • Matched by: Abyss
MacPorts ports tree · api.github.com · MacPorts ports tree: www/abyss/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • btllibRuntime dependency declared by Homebrew.
  • open-mpiRuntime dependency declared by Homebrew.

Same workflow

  • flyeShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
  • spadesShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
  • polypolishShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science, short-reads.
  • bwaShares av.db curated category or tags: bioinformatics, cli, science, short-reads.
  • abpoaShares av.db curated category or tags: bioinformatics, cli, science.
  • abricateShares av.db curated category or tags: bioinformatics, cli, science.

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.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment