使用 Homebrew, apt, MacPorts 安装 abyss

项目链接

• 主页
• 仓库
• 上游文档
• 软件包管理器页面

命令和别名

• 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

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• 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