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You are here : Home / Home URGI / Research / Repeat annotation / Publications / Tedna: a Transposable Element De Novo Assembler.

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International,  ACL (papers with reading comittee)

Bioinformatics. 2014 Jun 3. pii: btu365

PMID:24894500

03 Jun 2014   Tedna: a Transposable Element De Novo Assembler.

Zytnicki M, Akhunov E, Quesneville H

MOTIVATION:

Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain very high proportions of transposable elements, and transposable elements appear to be a major force behind diversity and adaptation. Few de novo assemblers for transposable elements exist, and most have either been designed for small genomes or 454 reads.

RESULTS:

In this paper, we present a new transposable element de novo assembler, Tedna, which assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full length transposable elements. Availability: Tedna is available from http://urgi.versailles.inra.fr/Tools/Tedna, under the GPLv3 license. It is written in C++11 and only requires the sparsehash package, freely available under the New BSD License. Tedna can be used on standard computers with limited RAM resources, although it may also use large memory for better results. Most of the code is parallelized, and thus ready for large infrastructures.


Creation date: 12 Jun 2014
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