arq5x/bedtools2

Health v2 · maintenance only

Adoption not part of the score

1045 stars · 293 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

bedtools is a suite of command-line utilities for genome arithmetic, enabling set-theory operations like intersect, merge, count, complement, and shuffle on genomic intervals in formats such as BED, BAM, GFF/GTF, and VCF. Written in C++, it scales efficiently on sorted data and composes well with UNIX pipelines for sophisticated genomics analyses.

Use cases

• intersect two genomic interval files
• merge overlapping bed intervals
• count reads overlapping exons from a bam file
• shuffle genomic intervals for permutation testing
• complement a set of genomic regions
• convert and compare annotations across bed gff vcf formats

When to choose

• you need fast set operations on genomic intervals from the command line
• you want to build complex genomics pipelines by chaining unix tools
• you work with large sorted BAM/BED datasets and need scalable performance

When to avoid

• you need a graphical interface for genomic analysis
• you require statistical genomics modeling beyond interval arithmetic
• you prefer a library API in Python or R rather than CLI tools

Facets

cli-tool · maturity stable

cli parser developer-tools bioinformatics data-science cpp cli genomics bed bam vcf gff genome-arithmetic bioinformatics interval-operations command-line linux macos

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