bedtools
suite of utilities for comparing genomic features
Command lineScience
Not tested on a device yet. What that means
Commands in the package
bedtoolsannotateBedbamToBedbamToFastqbed12ToBed6bedToBambedToIgvbedpeToBamclosestBedclusterBedcomplementBedcoverageBedexpandColsfastaFromBedflankBedgenomeCoverageBedgetOverlapgroupByintersectBedlinksBedmapBedmaskFastaFromBedmergeBedmultiBamCovmultiIntersectBednucBedpairToBedpairToPairrandomBedshiftBedshuffleBedslopBedsortBedsubtractBedtagBamunionBedGraphswindowBedwindowMaker
About bedtools
From Debian's package description
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.
The groupBy utility is distributed in the filo package.
From Debian's description of the bedtools package, under that package's license.
Dependencies
Depends on
libbz2-1.0libc6libgcc-s1liblzma5libstdc++6zlib1g
Related apps
- bamkittools for common BAM file manipulationsCommand line
- cctvisually comparing bacterial, plasmid, chloroplast, or mitochondrial sequencesCommand line
- bcftoolsgenomic variant calling and manipulation of VCF/BCF filesCommand line
- FastQC quality controlquality control for high throughput sequence data
igvdesktop genome vizualisation tool
SeaViewEdits multiple sequence alignments and prints them in PostScript format.
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the bedtools package, under that package's license.
- Description: Debian's description of the bedtools package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.