An Index for Sequencing Reads Based on The Colored de Bruijn Graph

Abstract: 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.