RT Journal Article
SR Electronic
T1 Scalable multi whole-genome alignment using recursive exact matching
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 022715
DO 10.1101/022715
A1 Jasper Linthorst
A1 Marc Hulsman
A1 Henne Holstege
A1 Marcel Reinders
YR 2015
UL http://biorxiv.org/content/early/2015/07/17/022715.abstract
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