bedops ☆
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Description:
Set and statistical operations on genomic data of arbitrary scale
Type: Formula  |  Latest Version: 2.4.42@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: genomics bioinformatics bedops genomic-data command-line
Install: brew install bedops
About:
BEDOPS is a suite of high-performance command-line tools for genomic interval arithmetic and data processing. It efficiently performs set operations like intersections, unions, and differences on genomic data files such as BED, GFF, and VCF formats. The toolkit is optimized for speed and low memory usage, making it ideal for large-scale bioinformatics workflows.
Key Features:
  • High-performance set operations on genomic intervals
  • Support for multiple formats (BED, GFF, VCF, SAM)
  • Optimized for low memory footprint and speed
  • Modular command-line tools for flexible workflows
Use Cases:
  • Identifying overlaps between gene annotations and ChIP-seq peaks
  • Filtering and comparing genetic variants from VCF files
  • Preparing input data for downstream analysis tools
Alternatives:
  • bedtools – bedtools is another popular toolkit for genomic arithmetic, but BEDOPS is often faster and uses less memory for large datasets.
License: GPL-2.0-or-later
Dependencies: jansson
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, sonoma, ventura, arm64_linux, x86_64_linux
Version History
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