REAL: an efficient REad ALigner for next generation sequencing reads

Authors:
Kimon Frousios;Costas S. Iliopoulos;Laurent Mouchard;Solon P. Pissis;German Tischler
Affiliations:
King's College London, London, England, United Kingdom;King's College London, London, England, United Kingdom;Université de Rouen, Mont Saint Aignan, France;King's College London, London, England, United Kingdom;King's College London, London, England, United Kingdom
Venue:
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Year:
2010

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Abstract

Motivation: The constant advances in sequencing technology are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data in the form of short reads need to be mapped back to reference sequences, a few gigabases long. A first generation of short read alignment software successfully employed hash tables, and the current second generation uses Burrows-Wheeler Transform, further improving mapping speed. However, there is still demand for faster and more accurate mapping. Results: In this paper, we present REad ALigner, an efficient, accurate and consistent tool for aligning short reads obtained from next generation sequencing. It is based on a new, simple, yet efficient mapping algorithm that can match and outperform current BWT-based software.