Dynamic construction of pan-genome subgraphs

Abstract

Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph as a description of a pan-genome, comprising the genomes of many individuals/strains of the same or closely related species. Subsequent work improved the construction of the compressed de Bruijn graph in terms of run-time and memory consumption. According to the Computational Pan-Genomics Consortium (Briefings in Bioinformatics 2016), a pan-genome data structure should support the following functionality: “All information within a data structure should be easily accessible for human eyes by visualization support on different scales.” However, a pan-genome graph can have thousands to millions of nodes and such an amount of information is certainly not easily accessible for human eyes. Thus, the possibility to construct pangenome subgraphs on demand would be quite valuable. In this article, we use the space-efficient representation of the compressed de Bruijn graph devised by Beller and Ohle-busch (Algorithms for Molecular Biology 2016) to construct pan-genome subgraphs on the fly. The user can specify a region in one of the genomes and the software tool will build a subgraph that contains the path corresponding to that region and all paths that are in the neighborhood of that path. The size of the neighborhood can be controlled by the user.

Keywords

• compressed de bruijn graph
• burrows-wheeler transform
• backward search
• pan-genome analysis