10. Related software

### Navigation

- index
- previous |
- bedtools v2.18.0 »

# 10. Related software

Bedtools has been used as an engine behind other genomics software and has been integrated into widely used tools such as Galaxy and IGV. Below is a likely incomplete list. If you know of others, please let us know, or better yet, edit the document on GitHub and send us a pull request. You can do this by clicking on the “Edit and improve this document” link in the lower lefthand corner.

## 10.1. IGV

Bedtools is now integrated into the IGV genome viewer as of IGV version 2.2. We are actively working withe IGV development team to improve and expand this integration. See here and here for details.

## 10.2. Galaxy

Galaxy has its own tools for working with genomic intervals under the “Operate on Genomic Intervals” section. A subset of complementary Bedtools utilities have also been made available on Galaxy in an effort to provide functionality that isn’t available with the native Galaxy tools.

## 10.3. Pybedtools

Pybedtools is a really fantastic Python library that wraps (and extends upon) the bedtools utilities and exposes them for easy use and new tool development using Python. Pybedtools is actively maintained by Ryan Dale.

## 10.4. MISO

MISO is “a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.” A subset of the functionality in MISO depends upon `bedtools`. MISO is developed by Yarden Katz.

## 10.5. RetroSeq

RetroSeq is “a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format”. RetroSeq is developed by Thomas Keane. Source code can be obtained on GitHub.

comments powered by Disqus

### Navigation

- index
- previous |
- bedtools v2.18.0 »

### Edit and improve this document!

This file can be edited directly through the Web. Anyone can update and fix errors in this document with few clicks -- no downloads needed.

1. Go to 10. Related software on GitHub.
2. Edit files using GitHub's text editor in your web browser (see the 'Edit' tab on the top right of the file)
3. Fill in the Commit message text box at the bottom of the page describing why you made the changes. Press the Propose file change button next to it when done.
4. Then click Send a pull request.
5. Your changes are now queued for review under the project's Pull requests tab on GitHub!

For an introduction to the documentation format please see the reST primer.