INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
Bioinformatics. 2014 Sep 15;30(18):2656-8. doi: 10.1093/bioinformatics/btu365. Epub 2014 Jun 3.
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.
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.
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.
最近的技术进步使得许多实验室能够对其研究生物进行测序。现有的从头组装程序会导致基因组的重复部分组装得很差。有些基因组包含大量转座元件，而转座元件似乎是多样性和适应性的主要驱动力。现有的转座元件从头组装程序很少，而且大多数程序要么是为小基因组设计的，要么是为 454 读取设计的。
在本文中，我们提出了一种新的转座元件从头组装程序 Tedna，它可以直接从读取序列中组装一组转座元件。Tedna 使用 Illumina 配对末端读取，这是最广泛用于从头组装的测序技术，并形成全长转座元件。
Tedna 可在 http://urgi.versailles.inra.fr/Tools/Tedna 获得，遵循 GPLv3 许可证。它是用 C++11 编写的，只需要 Sparsehash 包，它可以在新的 BSD 许可证下免费获得。Tedna 可以在具有有限 RAM 资源的标准计算机上使用，尽管它也可能需要大量内存以获得更好的结果。大多数代码都进行了并行化处理，因此可以在大型基础设施上使用。
