badread ☆
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Description:
Long read simulator that can imitate many types of read problems
Type: Formula  |  Latest Version: 0.4.1@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics simulation genomics long-read-sequencing research
Install: brew install badread
About:
Badread is a versatile long-read simulator designed to generate realistic synthetic sequencing data. It accurately models various error profiles, including chimeras, low-quality reads, and random fragments. This tool is essential for benchmarking bioinformatics pipelines and testing assembly algorithms under controlled conditions.
Key Features:
  • Simulates diverse error types (chimeras, low quality, random fragments)
  • Supports both reference-based and random sequence generation
  • Highly configurable via command-line arguments
  • Generates FASTQ output compatible with standard tools
Use Cases:
  • Benchmarking genome assembly algorithms with noisy data
  • Testing the robustness of variant calling pipelines
  • Generating test data for bioinformatics training
Alternatives:
  • PBSIM3 – PBSIM3 simulates PacBio reads using reference sequences, while Badread offers more granular control over error rates and random generation.
  • NanoSim – NanoSim focuses specifically on Oxford Nanopore reads, whereas Badread provides a more generalized simulation approach.
License: GPL-3.0-or-later
Dependencies: numpy, python@3.14, scipy
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, sonoma, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Oct 27, 2025 11:42pm 0 VERSION_BUMP efec2403
Sep 13, 2025 11:32am 0 VERSION_BUMP ad67d60d
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