Matthias Zytnicki1, Eduard Akhunov1, Hadi Quesneville1. 1. INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
Abstract
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 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 article, 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 AND IMPLEMENTATION: Tedna is available at 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.
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 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 article, 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 AND IMPLEMENTATION: Tedna is available at 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.
Authors: Douglas R Hoen; Glenn Hickey; Guillaume Bourque; Josep Casacuberta; Richard Cordaux; Cédric Feschotte; Anna-Sophie Fiston-Lavier; Aurélie Hua-Van; Robert Hubley; Aurélie Kapusta; Emmanuelle Lerat; Florian Maumus; David D Pollock; Hadi Quesneville; Arian Smit; Travis J Wheeler; Thomas E Bureau; Mathieu Blanchette Journal: Mob DNA Date: 2015-08-04
Authors: Agata Weydmann; Aleksandra Przyłucka; Marek Lubośny; Katarzyna S Walczyńska; Ester A Serrão; Gareth A Pearson; Artur Burzyński Journal: Sci Rep Date: 2017-10-20 Impact factor: 4.379
Authors: Jakub Wudarski; Daniil Simanov; Kirill Ustyantsev; Katrien de Mulder; Margriet Grelling; Magda Grudniewska; Frank Beltman; Lisa Glazenburg; Turan Demircan; Julia Wunderer; Weihong Qi; Dita B Vizoso; Philipp M Weissert; Daniel Olivieri; Stijn Mouton; Victor Guryev; Aziz Aboobaker; Lukas Schärer; Peter Ladurner; Eugene Berezikov Journal: Nat Commun Date: 2017-12-14 Impact factor: 14.919