Command-line tool

bedtools

brew/bedtools

Checked 25 Oct 2026, 21:09 UTC · Listing refreshed from Homebrew, winget, npm, Scoop and cargo; npm packages checked against OSV.dev

Tools for genome arithmetic (set theory on the genome)

Website Source

At a glance

Type

Command-line tool

Install on

macOS, Linux

Last checked

25 Oct 2026, 21:09 UTC

Install it

macOS

brew install bedtools

Linux

brew install bedtools

Intersect file [a] and file(s) [b] regarding the sequences' [s]trand and save the result to a specific file

bedtools intersect -a path/to/file_A -b path/to/file_B1 path/to/file_B2 ... -s > path/to/output_file

Intersect two files with a [l]eft [o]uter [j]oin, i.e. report each feature from `file1` and NULL if no overlap with `file2`

bedtools intersect -a path/to/file1 -b path/to/file2 -loj > path/to/output_file

Use a more efficient algorithm to intersect two pre-sorted files

bedtools intersect -a path/to/file1 -b path/to/file2 -sorted > path/to/output_file

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  Burrow-Wheeler Aligner for pairwise alignment of DNA
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• fastani
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• sylph
  Ultrafast taxonomic profiling and genome querying for metagenomic samples
• theory_grabber
  Downloads papers from arxiv and eccc and stores them in a local directory. Saves the last date looked at.
• autocycler
  Tool for generating consensus long-read assemblies for bacterial genomes
• plink-ng
  Whole-genome association analysis toolset (PLINK 2.0)
• skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs

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