TY - JOUR T1 - Scalable multi whole-genome alignment using recursive exact matching JF - bioRxiv DO - 10.1101/022715 SP - 022715 AU - Jasper Linthorst AU - Marc Hulsman AU - Henne Holstege AU - Marcel Reinders Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/07/17/022715.abstract N2 - 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 ER -