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Summary

This set of programs allows one to identify transposable element insertions (TEI) in a sequenced sample with respect to an assembled reference.

The main script jitterbug.py performs this analysis, using a .bam file of mapped reads and the annotation of TEs in the reference.

Additional modules are provided to filter and plot these results, compare tumor/normal pairs as well evaluate predictions from simulated data.

To access the release version corresponding to the related publication in BMC Genomics:

// clone the repository
git clone git://git.code.sf.net/p/jitterbug/code jitterbug-code

//list the available tags
git tag -l

//move to the version tagged with v1.0
git checkout tags/v1.0

Information on dependencies, installation and usage are available in that version's README

Enjoy!

Project Admins:

• elizabeth henaff
• Stephan Ossowski