Scalable multi whole-genome alignment using recursive exact matching

Jasper Linthorst; Marc Hulsman; Henne Holstege; Marcel Reinders

doi:10.1101/022715

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bioRxiv · 10.1101/022715

Scalable multi whole-genome alignment using recursive exact matching

Jasper Linthorst·Marc Hulsman·Henne Holstege·Marcel Reinders

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Abstract

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.\n\nIn 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.\n\nWe 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.\n\nAn implementation of the outlined algorithm called REVEAL is available on: https://github.com/jasperlinthorst/REVEAL

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Jasper Linthorst, Marc Hulsman, Henne Holstege, Marcel Reinders. 2015-07-17. Scalable multi whole-genome alignment using recursive exact matching. https://doi.org/10.1101/022715

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