PE-Assembler: de novo assembler using short paired-end reads
PE-Assembler: de novo assembler using short paired-end reads
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DOI：
10.1093/bioinformatics/btq626
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发表时间：
2011-01-15
期刊：
影响因子：
5.8
通讯作者：
Sung, Wing-Kin
中科院分区：
文献类型：
--
作者：
Ariyaratne, Pramila Nuwantha;Sung, Wing-Kin
动机：最近提出了许多从头基因组组装。大多数现有方法的基础依赖于de bruijn图：一种试图包含整个基因组的复杂图结构。这样的图可以是过大，可能无法捕捉到微妙的信息，是难以并行化的。结果：我们提出了一种方法，避免了传统的基于图的方法，有利于一个简单的3'扩展的方法，有可能被大规模并行化。我们的研究结果表明，它是能够获得更连续，完整和更少的错误倾向与现有的方法相比，组件。
Motivation: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.Result: We present a method that eschews the traditional graph-based approach in favor of a simple 3' extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods.