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

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).