Simplitigs as an efficient and scalable representation of de Bruijn graphs

Abstract:

Motivation De Bruijn graphs play an essential role in computational biology, facilitating rapid alignment-free comparison of genomic datasets as well as reconstruction of underlying genomic sequences. Subsequently, an important question is how to efficiently represent, compress, and transmit de Bruijn graphs of the most common types of genomic data sets, such as sequencing reads, genomes, and pan-genomes.

Results We introduce simplitigs, an effective representation of de Bruijn graphs for alignment-free applications. Simplitigs are a generalization of unitigs and correspond to spellings of vertex-disjoint paths in a de Bruijn graph. We present an easy-to-plug-in greedy heuristic for their computation and provide a reference implementation in a program called ProphAsm. We use ProphAsm to compare the scaling of simplitigs and unitigs on a range of genomic datasets. We demonstrate that simplitigs are superior to unitigs in terms of the cumulative sequence length as well as of the number of sequences, and that they are sufficiently close to the theoretical bounds for practical applications. Finally, we demonstrate that, when combined with standard full-text indexes, simplitigs provide a scalable solution for k-mer search in pan-genomes.

Availability ProphAsm is written in C++ and is available under the MIT license from http://github.com/prophyle/prophasm.

Publisher's Version

Last updated on 03/06/2020