abyss ☆
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Description:
Genome sequence assembler for short reads
Type: Formula  |  Latest Version: 2.3.10@1  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics assembly sequence-analysis hpc
Install: brew install abyss
About:
ABySS (Assembly By Short Sequences) is a de novo sequence assembler designed for short paired-end reads. It utilizes a de Bruijn graph approach to efficiently assemble large genomes, making it suitable for projects with substantial computational requirements. The tool is particularly effective for handling the complexities of large and repetitive genomic regions.
Key Features:
  • Scalable de Bruijn graph assembly
  • Integrated support for paired-end and long-read data
  • Optimized for high-performance computing (MPI)
  • Includes tools for error correction and scaffolding
Use Cases:
  • De novo genome assembly for non-model organisms
  • Resequencing analysis and variant detection
  • Metagenomic assembly of microbial communities
Alternatives:
  • SPAdes – SPAdes is often preferred for smaller genomes or when hybrid assembly (short + long reads) is required, while ABySS excels at scaling for very large genomes on HPC clusters.
  • Velvet – Velvet is a classic assembler that uses similar graph-based methods, but ABySS is specifically designed for distributed memory systems to handle larger datasets.
License: GPL-3.0-only AND LGPL-2.1-or-later AND MIT AND BSD-3-Clause
Dependencies: btllib, open-mpi
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, sonoma, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Oct 23, 2025 2:21pm 1 VERSION_BUMP 7d3cd598
Sep 13, 2025 9:22am 0 VERSION_BUMP 19cc1b73
Sep 14, 2024 1:25pm 0 VERSION_BUMP cdafca53
Sep 14, 2024 8:39am 0 VERSION_BUMP d2f3beb0
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