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arXiv 1003.1940cs.DScs.DC
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构造大型双向de Bruijn图的高效并行和核外算法

Efficient Parallel and Out of Core Algorithms for Constructing Large Bi-directed de Bruijn Graphs

Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh

摘要:

从一组重叠读段组装基因组序列是计算生物学中最基本的问题之一。解决装配问题的算法根据它们所采用的数据结构分为两大类。第一类使用重叠/字符串图,第二类使用de Bruijn图。然而,随着短读段测序技术的最新进展,基于de Bruijn图的算法似乎在实践中发挥着至关重要的作用。构建这些大规模de Bruijn图的有效算法在基于短读段的大型测序项目中非常重要。在Jackson et. al. ICPP-2008中,给出了该问题的一个$O(n/p)$时间并行算法。这里,$n$是输入的大小,$p$是处理器的数量。该算法枚举所有可能与节点重叠的双向边,并最终生成$Θ(nΣ)$消息。本文提出了一种$Θ(n/p)$时间并行算法,它的通信复杂度等于并行排序的通信复杂度,并且对$Σ$不敏感。我们的算法的通用性使得它很容易扩展到外的核心模型,在这种情况下,它有一个最佳的I/O复杂度为$Θ(\frac{n\log(n/B)}{B\log(M/B)})$。我们证明了我们的并行算法在SGI/Altix计算机上的可扩展性。我们的算法与Jackson等的比较。ICPP-2008表明,我们的算法更快。我们还提供了有效的算法的双向链压缩问题。

英文摘要:

Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In Jackson et. al. ICPP-2008, an $O(n/p)$ time parallel algorithm has been given for this problem. Here $n$ is the size of the input and $p$ is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating $Θ(nΣ)$ messages. In this paper we present a $Θ(n/p)$ time parallel algorithm with a communication complexity equal to that of parallel sorting and is not sensitive to $Σ$. The generality of our algorithm makes it very easy to extend it even to the out-of-core model and in this case it has an optimal I/O complexity of $Θ(\frac{n\log(n/B)}{B\log(M/B)})$. We demonstrate the scalability of our parallel algorithm on a SGI/Altix computer. A comparison of our algorithm with that of Jackson et. al. ICPP-2008 reveals that our algorithm is faster. We also provide efficient algorithms for the bi-directed chain compaction problem.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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