Install bedops with Homebrew, apt, Nix

Project links

• Homepage
• Upstream docs
• Package manager page

Commands and aliases

• bam2bed
• bam2bed_gnuParallel
• bam2bed_sge
• bam2bed_slurm
• bam2starch
• bam2starch_gnuParallel
• bam2starch_sge
• bam2starch_slurm
• bedextract
• bedmap
• bedops
• closest-features
• convert2bed
• gff2bed
• gff2starch
• gtf2bed
• gtf2starch
• gvf2bed
• gvf2starch
• psl2bed
• psl2starch
• rmsk2bed
• rmsk2starch
• sam2bed
• sam2starch
• sort-bed
• starch
• starch-diff
• starchcat
• starchcluster_gnuParallel
• starchcluster_sge
• starchcluster_slurm

Project history

BEDOPS grew out of genomics workflows that needed efficient Boolean and statistical operations over large BED-like datasets. The upstream documentation describes it as a toolkit for arbitrary-scale genomic data, built around sorted BED data, streaming Unix I/O, and chromosome-level partitioning.

The project was published in Bioinformatics in 2012 as 'BEDOPS: high-performance genomic feature operations.' The GitHub repository dates to 2013, while copyright and documentation history identify the project line as active from 2011 onward.

A major part of BEDOPS history is the Starch archive format, which the docs describe as lossless compression with metadata and random access by chromosome. That made the suite more than a set-operations command: it became a file-management layer for large interval collections.

Adoption history

BEDOPS is packaged for Homebrew, Debian, Ubuntu, and Nix in the supplied metadata. Its official installation documentation also documents Homebrew, Bioconda, Docker, source builds, and prebuilt binaries, reflecting adoption in both workstation and cluster-style bioinformatics environments.

The revision history shows sustained maintenance across the v2.4 series, including large-input sorting fixes, conversion fixes for GTF/GFF/WIG/SAM/BAM-derived formats, GitHub Actions migration, and a v2.4.42 release in April 2025.

How it is used

Typical BEDOPS use chains tools such as bedops, bedmap, closest-features, sort-bed, starch, unstarch, and format converters through standard input and output. The docs emphasize streaming pipelines, per-chromosome work splitting, and map-reduce-style parallelization.

BEDOPS is most valuable when researchers need to intersect, merge, subtract, complement, map, summarize, compress, or convert large genomic feature datasets without loading entire whole-genome inputs into memory.

Why package nerds care

BEDOPS matters to package nerds because it is a classic Unix-philosophy scientific toolkit: many specialized binaries, streamable text interfaces, stable file conventions, and performance claims that matter directly to package users handling large local datasets.

It is also a useful contrast with bedtools. Both live in the genomic-interval ecosystem, but BEDOPS leans hard into sorted data, low memory overhead, Starch compression, and easy chromosome-level parallelism, making packaging details such as compiler support, binary type, and converter scripts unusually important.

Timeline

• 2011: BEDOPS project line begins, per upstream copyright and documentation history.
• 2012: BEDOPS paper published in Bioinformatics.
• 2013: GitHub repository created.
• 2021: v2.4.40 migrated CI to GitHub Actions and continued converter/starch maintenance.
• 2022: v2.4.41 released with compiler and conversion fixes.
• 2025: v2.4.42 released.

Related projects

• bedtools is the closest peer in genome arithmetic and interval manipulation.
• BED, BAM, SAM, GFF, GTF, VCF, WIG, and Starch are central formats in BEDOPS workflows.
• Bioconda, Homebrew, Debian, Ubuntu, and Nix are relevant distribution channels for command-line bioinformatics users.

Sources

• https://api.github.com/repos/bedops/bedops
• https://bedops.readthedocs.io/en/latest
• https://bedops.readthedocs.io/en/latest/content/overview.html
• https://bedops.readthedocs.io/en/latest/content/revision-history.html
• https://github.com/bedops/bedops#readme
• source_facts.package-manager