Fast mapping and precise alignment of AB SOLiD color reads to reference DNA

Authors:
Miklós Csürös;Szilveszter Juhos;Attila Bérces
Affiliations:
Department of Computer Science and Operations Research, University of Montréal, Canada;Omixon, Budapest, Hungary;Omixon, Budapest, Hungary
Venue:
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Year:
2010

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Abstract

Applied Biosystems' SOLiD system offers a low-cost alternative to the traditional Sanger method of DNA sequencing. We introduce two main algorithms of mapping SOLiD's color reads onto a reference genome. The first method performs mapping by adapting a greedy alignment framework. In such an alignment, reads are mapped to approximate genome positions, allowing for a pre-specified bound on sequence difference that combines nucleotide mismatches, gaps, and sequencing errors. The second method for precise alignment relies on a pair hidden Markov model framework, combining a DNA sequence evolution model and sequencing errors (from read quality files).