# arq5x/bedtools2

bedtools - the swiss army knife for genome arithmetic

Repository: https://github.com/arq5x/bedtools2
Canonical: https://ross.abutalabs.com/products/bedtools2
Language: C
License: MIT
License Family: permissive
Last push: 2026-06-10T22:16:43+00:00

## Health v2 (maintenance only)
Score: 62/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 86, release rhythm 8, longevity 100
- inputs: {"age_days": 4650, "days_push": 84, "days_rel": null, "gap_med": null, "n_releases_24m": 0}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1045, forks 293 (observed 2026-08-28T04:03:21.428101+00:00)

## What it is
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
- artifact type: cli-tool
- maturity: stable
- function: cli, parser, developer-tools
- domain: bioinformatics, data-science
- platform: cpp, cli
- tags: genomics, bed, bam, vcf, gff, genome-arithmetic, bioinformatics, interval-operations, command-line, linux, macos

## Member repositories
- arq5x/bedtools2 (main) score 62

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:03:21.428101+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T07:02:03.310694+00:00, confidence not recorded.
  - readme: https://github.com/arq5x/bedtools2 (fetched 2026-08-28T04:03:21.428101+00:00, sha 3e49b10f8769)
- Data as of 2026-08-30T08:39:29.467469+00:00.