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Repository bedtools
Name: bedtools
Owner: iuc
Synopsis: bedtools is a powerful toolset for genome arithmetic
Collectively, 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. While
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.
Clone this repository: hg clone
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Contents of this repository

Name Description Version Minimum Galaxy Version
annotate coverage of features from multiple files 2.29.2 16.01
converter 2.29.2 16.01
converter 2.29.2 16.01
converter 2.29.2 16.01
create batch script for taking IGV screenshots 2.29.2 16.01
converter 2.29.2 16.01
find the closest, potentially non-overlapping interval 2.29.2 16.01
cluster overlapping/nearby intervals 2.29.2 16.01
Extract intervals not represented by an interval file 2.29.2 16.01
of features in file B on the features in file A (bedtools coverage) 2.29.2 16.01
replicate lines based on lists of values in columns 2.29.2 16.01
calculate Fisher statistic between two feature files 2.29.2 16.01
create new intervals from the flanks of existing intervals 2.29.2 16.01
compute the coverage over an entire genome 2.29.2 16.01
use intervals to extract sequences from a FASTA file 2.29.2 16.01
group by common cols and summarize other cols 2.29.2 16.01
find overlapping intervals in various ways 2.29.2 16.01
calculate the distribution of relative distances between two files 2.29.2 16.01
create a HTML page of links to UCSC locations 2.29.2 16.01
make interval windows across a genome 2.29.2 16.01
apply a function to a column for each overlapping interval 16.01
use intervals to mask sequences from a FASTA file 2.29.2 16.01
combine overlapping/nearby intervals into a single interval 2.29.2 16.01
counts coverage from multiple BAMs at specific intervals 2.29.2 16.01
identifies common intervals among multiple interval files 2.29.2 16.01
profile the nucleotide content of intervals in a FASTA file 2.29.2 16.01
computes the amount of overlap from two intervals 2.29.2 16.01
generate random intervals in a genome 2.29.2 16.01
calculate the distribution of relative distances 2.29.2 16.01
randomly redistrubute intervals in a genome 2.29.2 16.01
adjust the size of intervals 2.29.2 16.01
order the intervals 2.29.2 16.01
reports the distances between features 2.29.2 16.01
remove intervals based on overlaps 2.29.2 16.01
tag BAM alignments based on overlaps with interval files 2.29.2 16.01
combines coverage intervals from multiple BEDGRAPH files 2.29.2 16.01
find overlapping intervals within a window around an interval 2.29.2 16.01

Text Manipulation - Tools for manipulating data
Genomic Interval Operations - Tools for operating on genomic intervals