一种基于着色de Bruijn图的读序索引
An Index for Sequencing Reads Based on The Colored de Bruijn Graph
摘要：
在这篇文章中，我们展示了如何将彩色de Bruijn图（dBG）转换为用于处理大量测序读数的实用索引。与以前的工作类似，我们使用BOSS和颜色矩阵C对集合的彩色dBG的实例进行编码。为了减少空间需求，我们设计了一个算法，产生一个更小，更稀疏的C语言版本。该算法的新颖之处在于（i）图的不完全着色和（ii）贪婪着色方法，该方法试图在可能的情况下为不同的字符串重用相同的颜色。我们还提出了两种算法，工作在顶部的索引;一个是重建读取，另一个是重叠群组装。实验结果表明，我们的数据结构使用了大约一半的空间的平原表示的集合（1字节每个DNA符号），超过99%的读取可以重建只是从索引。
英文摘要：
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a color matrix C. To reduce the space requirements, we devise an algorithm that produces a smaller and more sparse version of C. The novelties in this algorithm are (i) an incomplete coloring of the graph and (ii) a greedy coloring approach that tries to reuse the same colors for different strings when possible. We also propose two algorithms that work on top of the index; one is for reconstructing reads, and the other is for contig assembly. Experimental results show that our data structure uses about half the space of the plain representation of the set (1 Byte per DNA symbol) and that more than 99% of the reads can be reconstructed just from the index.
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