<p>Hi,</p>

<p>I finished mapping and variant calling on these for solid data. Now I&#39;m looking to identify large rearrangements and transposable elements. Can anyone tell me any good tools for these? One tool I have come across now is <a href="https://code.google.com/p/nfuse/">nFuse</a>. I wanted to know what the general pipeline for this is.</p>

<p>And I would like to view such arrangements as <code>Circos</code> plots.</p>

<p>Thanks for the help.</p>

There are a number of non-reference TE insertion mapping tools available now including:

 - [RelocaTE](https://github.com/stajichlab/RelocaTE)
 - [ngs_te_mapper](https://github.com/bergmanlab/ngs_te_mapper)
 - [PoPoolationTE](https://code.google.com/p/popoolationte/)
 - [TE-locate](http://sourceforge.net/projects/te-locate/)
 - [RetroSeq](https://github.com/tk2/RetroSeq)
 - [TEMP](https://github.com/JialiUMassWengLab/TEMP)

These systems differ in how they map NGS reads, how they discover and represent non-reference TEs in a genome (see <a href="https://www.biostars.org/p/49563/">https://www.biostars.org/p/49563/</a>), and in their final output file formats. We have tried to characterise the major features of each of these systems (besides TEMP) in <a href="http://figshare.com/articles/A_review_of_methods_for_detecting_non_reference_transposable_element_insertions_from_high_throughput_genome_resequencing_data_/831475">this poster</a>. There has been no systematic evaluation of all of these methods, so it is difficult to say which is the "best".

In the absence of a thorough evaluation study, our view is that it is necessary to run multiple TE mapping tools and evaluate the impact that different tools have on your biological conclusions. To this end, we are currently developing a meta-pipeline called <a href="https://github.com/bergmanlab/mcclintock">McClintock</a> that installs and runs all of the tools listed above (besides TEMP) and outputs results in a standard BED format.