Simulating the DNA String Graph in Succinct Space
Abstract
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has advantages over the other depending on the application. Still, the ideal setting would be to have an index of the reads that is easy to build and can be adapted to any type of biological analysis. In this paper, we propose a new data structure we call rBOSS, which gets close to that ideal. Our rBOSS is a de Bruijn graph in practice, but it simulates any length up to k and can compute overlaps of size at least m between the labels of the nodes, with k and m being parameters. If we choose the parameter k equal to the size of the reads, then we can simulate a complete string graph. As most BWTbased structures, rBOSS is unidirectional, but it exploits the property of the DNA reverse complements to simulate bidirectionality with some timespace tradeoffs. We implemented a genome assembler on top of rBOSS to demonstrate its usefulness. Our experimental results show that using k = 100, rBOSS can assemble 185 MB of reads in less than 15 minutes and using 110 MB in total. It produces contigs of mean sizes over 10,000, which is twice the size obtained by using a pure de Bruijn graph of fixed length k.
 Publication:

arXiv eprints
 Pub Date:
 January 2019
 arXiv:
 arXiv:1901.10453
 Bibcode:
 2019arXiv190110453D
 Keywords:

 Computer Science  Data Structures and Algorithms;
 J.3;
 E.1;
 G.2.2;
 J.3;
 E.1;
 G.2.2
 EPrint:
 This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie SklodowskaCurie Actions H2020MSCARISE2015 BIRDS GA No. 690941