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To tackle the exponentially increasing throughput of Next-GenerationSequencing (NGS), most of the existing short-read aligners can be configured tofavor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveragingthe computational power of both CPU and GPU with optimized algorithms, delivershigh speed and sensitivity simultaneously. Compared with widely adoptedaligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners includingBarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, whilemaintaining the highest sensitivity and lowest false discovery rate (FDR) onIllumina reads with different lengths. Transcending its predecessor SOAP3,which does not allow gapped alignment, SOAP3-dp by default tolerates alignmentsimilarity as low as 60 percent. Real data evaluation using human genomedemonstrates SOAP3-dp's power to enable more authentic variants and longerIndels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newlydiscovered deletions. SOAP3-dp natively supports BAM file format and provides ascoring scheme same as BWA, which enables it to be integrated into existinganalysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf andTianhe-1A.

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner