Versions: [2.30.0]


Download        : docker pull
Compressed Size : 28MB


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.


Pull (Download)

To download the latest version of bedtools2 run,

docker pull

or to download a specific version of bedtools2 run,

docker pull


To run the container as an application run,

docker run --rm bedtools2 --version

or to run the container in an interactive session run,

docker run -it --rm bash

Mounting volumes between the container and your machine

To access files from your machine within the bedtools2 container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data bedtools2 /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.


If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC bedtools2 container here.