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Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data.
This tool allows you to infer the abundance of repeat types in the genome without a reference genome sequence.
To use Transposome, you will need Perl installed (version 5.10 or greater).
Staton SE, and Burke JM. 2015. Transposome: Annotation of transposable element families from unassembled sequence reads. Bioinformatics.