breseq ☆
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Description:
Computational pipeline for finding mutations in short-read DNA resequencing data
Type: Formula  |  Latest Version: 0.39.0@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics variant-calling evolution microbiology
Install: brew install breseq
About:
breseq is a computational pipeline for finding mutations in short-read DNA resequencing data. It predicts sequence mutations and genome rearrangements, including junctions formed by transposable elements. The tool generates HTML output for visualizing results and is widely used in microbial evolution experiments.
Key Features:
  • Identifies SNPs, indels, and structural variants
  • Predicts mutations in microbial genomes
  • Generates visual HTML reports
  • Handles junction detection for mobile elements
Use Cases:
  • Analyzing evolution of microbial populations
  • Identifying causal mutations in experimental evolution
  • Quality control of genome sequencing data
Alternatives:
  • Snippy – Faster variant calling but lacks breseq's detailed mutation prediction and visual reports
  • LoFreq – Better for detecting low-frequency variants but less focused on microbial evolution
License: GPL-2.0-or-later AND MIT AND BSD-3-Clause
Dependencies: bowtie2, r
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, sonoma, ventura, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Sep 14, 2025 6:32pm 0 VERSION_BUMP e029e37c
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