July 7, 2019  |  

Scalable multi whole-genome alignment using recursive exact matching

Authors: Linthorst, Jasper and Hulsman, Marc and Holstege, Henne and Reinders, Marcel

The emergence of third generation sequencing technologies has brought near perfect de-novo genome assembly within reach. This clears the way towards reference-free detection of genomic variations. In this paper, we introduce a novel concept for aligning whole-genomes which allows the alignment of multiple genomes. Alignments are constructed in a recursive manner, in which alignment decisions are statistically supported. Computational performance is achieved by splitting an initial indexing data structure into a multitude of smaller indices. We show that our method can be used to detect high resolution structural variations between two human genomes, and that it can be used to obtain a high quality multiple genome alignment of at least nineteen Mycobacterium tuberculosis genomes. An implementation of the outlined algorithm called REVEAL is available on: https://github.com/jasperlinthorst/REVEAL

Journal: BioRxiv
DOI: 10.1101/022715
Year: 2015

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