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18-04-2016 NEW version 1.2 available !!! See info & Download at GitHub here !!!

What is dnaPipeTE ?

dnaPipeTE, for De Novo Assembly & Annotation Pipeline for Transposable Elements, is a bioinformatic pipeline dedicated to find, annotate and quantify transposable elements as well as other repeated DNA, in NGS low coverage genomic datasets.

dnaPipeTE produces a global estimation of the main repeat classes proportion in the genome, it estimates the relative abundance of each assembled repeat and draw the TE age distribution for the most recent elements.

How does dnaPipeTE work ?

Repeated DNA, as transposable elements, is over-represented into genomic sequencing reads. dnaPipeTE uses the RNAseq assembler Trinity to build repeat contigs from small genomic samples (< 1X genome coverage). Using Trinity on genomic data allow to recover alternative TE consensus of one family by producing distinct contigs for each structural variant. It then annotates the repeats using RepeatMasker and quantifies their genome proportion from the sample.

The quantification of assembled repeats and the estimation of the total repeated content are performed separately, using an independent sample of the original dataset. In a first hand, the sampled reads are blasted against the dnaPipeTE contig to estimate their proportion in the genome, that could serve later to estimate the copy number. In a second hand, some elements could have not been assembled with Trinity (small copy number) but could be present in the sample (blue read in the figure below). Thus a second blast is performed against the dnaPipeTE contigs and a repeat database (Repbase is used by default)

What dnaPipeTE is NOT ?

dnaPipeTE is not sensu stricto a TE assembler : since low coverage sequencing is used, only the most repeated elements will be fully assembled. The less repeated families will be partially assembled. However, dnaPipeTE uses the number of reads mapping to the assembly to estimate the relative proportion of each repeat.

Forum and support

Be informed of latest news and get help with dnaPipeTE by registering to the forum : here