PT  - JOURNAL ARTICLE
AU  - Jasper Linthorst
AU  - Marc Hulsman
AU  - Henne Holstege
AU  - Marcel Reinders
TI  - Scalable multi whole-genome alignment using recursive exact matching
AID  - 10.1101/022715
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022715
4099  - http://biorxiv.org/content/early/2015/07/17/022715.short
4100  - http://biorxiv.org/content/early/2015/07/17/022715.full
AB  - 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