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Since the time of the HGP, research into next-generation sequencing, which can reduce the cost and time of sequence analysis using computer algorithms, has been actively conducted. Mapping is a next-generation sequencing method that identifies sequences by aligning short reads with a reference genome for which sequence information is known. Mapping can be applied to tasks such as SNP calling, motif searches, and gene identification. Research on mapping that utilizes BWT and GPU has been undertaken in order to obtain faster mapping. In this paper, we propose a new mapping algorithm with additional consideration for base swaps. The experimental results demonstrate that when the penalty score for swaps was −1, −2, and −3 in paired-end alignment, for the human whole genome, SOAP3-swap aligned 4667, 2318, and 972 more read pairs, respectively, than SOAP3-dp, and for the drosophila genome, SOAP3-swap aligned 1253, 454, and 129 more read pairs, respectively, than SOAP3-dp. SOAP3-swap has the same functionality as that of SOAP3-dp and also improves the alignment ratio by taking biologically significant swaps into account for the first time.

Reference Mapping Considering Swaps of Adjacent Bases