TwoPaCo：一个从多个完全基因组构建紧凑de Bruijn图的有效算法
TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes
摘要：
动机：De Bruijn图已经被提出作为一种数据结构，以便于在群体和比较基因组环境中分析相关的全基因组序列。然而，目前的方法不能很好地扩展到许多大尺寸的基因组（如哺乳动物基因组）。结果如下：在本文中，我们提出了TwoPaCo，一个简单的和可扩展的低内存算法直接从一组完整的基因组构建紧凑的de Bruijn图。我们证明了它可以在一个典型的共享内存机器上，在不到一天的时间内构建100个模拟人类基因组的图，在不到两个小时的时间内构建8个真正的灵长类动物的图。我们相信，这一进展将使数百个马达加斯加大小的基因组的新的生物学分析成为可能。可用性：我们的代码和数据可从github.com/medvedevgroup/TwoPaCo下载联系方式：ium125@psu.edu
英文摘要：
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes). Results: In this paper, we present TwoPaCo, a simple and scalable low memory algorithm for the direct construction of the compacted de Bruijn graph from a set of complete genomes. We demonstrate that it can construct the graph for 100 simulated human genomes in less then a day and eight real primates in less than two hours, on a typical shared-memory machine. We believe that this progress will enable novel biological analyses of hundreds of mammalian-sized genomes. Availability: Our code and data is available for download from github.com/medvedevgroup/TwoPaCo Contact: ium125@psu.edu
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