Project Highlight: SOAP3-dp

By a skillful exploitation of whole genome indexing and dynamic programming on a GPU, we devised a GPU-based tool called SOAP3-dp that can find alignments involving mismatches and INDELs, and it achieves a drastic improvement in speed and better sensitivity over all existing tools. In our experiments, when compared to BWA and the newly released Bowtie2, the speedup gained by SOAP3-dp ranges from 12 to 23 times. SOAP3-dp can align more reads than both tools for both single reads and paired-end reads. SOAP3-dp is also faster than its predecessor SOAP3 (allowing mismatches only) by 1.6 times, showing that GPU-based dynamic programming coupled with indexing can be much more efficient in dealing with reads with gaps and more mismatches.