bedtools

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  "desc": "Tools for genome arithmetic (set theory on the genome)",
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  "enrichment_fetched_at": "2026-06-20T23:35:49+00:00",
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  "full_name": "bedtools",
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  "github_last_commit_at": "2026-06-10T22:16:43Z",
  "github_readme_excerpt": "![shamalamadingdong](https://github.com/arq5x/bedtools2/blob/master/docs/bedtools.swiss.png \"foo\")\n\nbedtools - the swiss army knife for genome arithmetic         \n=====================================================\n\n[Download current version](https://github.com/arq5x/bedtools2/releases/latest)\n\n[Documentation](http://bedtools.readthedocs.org)\n\n[Cheat-sheet from Ilya Levantis](https://gist.github.com/ilevantis/6d6ecf8718a5803acff736c2dffc933e)\n\nSummary\n-------\nCollectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.\n\nWhile each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.\n\nPerformance\n-----------\nAs of version 2.18, ``bedtools`` is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are pre-sorted\nby chromosome and start position. As you can see in the plots below, the speed and memory consumption scale nicely\nwith sorted data as compared to the poor scaling for unsorted data. The current version of bedtools intersect is as fast as (or slightly faster) than the ``bedops`` package\u0027s ``bedmap`` which uses a similar algorithm for sorted data.  The plots below represent counting the number of intersecting alignments from exome capture BAM files against CCDS exons.\nThe alignments have been converted to BED to facilitate comparisons to ``bedops``. We compare to the bedmap ``--ec`` option because similar error checking is enforced by ``bedtools``.\n\n\n**Note:** bedtools could not complete when using 100 million alignments a",
  "github_repo": "arq5x/bedtools2",
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  "homepage": "https://github.com/arq5x/bedtools2",
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  "license": "MIT",
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  "name": "bedtools",
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  "ruby_source_path": "Formula/b/bedtools.rb",
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  "version_stable": "2.31.1",
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