./biology/bedtools, Swiss army knife for genome arithmetic

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Branch: CURRENT, Version: 2.30.0, Package name: bedtools-2.30.0, Maintainer: bacon

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.


Master sites:

SHA1: b3bae21434f261818e15875727b4a3c5c7366bc7
RMD160: 1cc30e5bc3df12f38d8f1e055ff2f939d7608395
Filesize: 20156.111 KB

Version history: (Expand)


CVS history: (Expand)


   2021-02-08 02:49:25 by Jason Bacon | Files touched by this commit (7) | Package updated
Log message:
biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
   2021-01-22 18:07:50 by Jason Bacon | Files touched by this commit (6)
Log message:
biology/bedtools: import bedtools-2.29.2

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.