Reconfigurable Hardware-based Genome Aligner Using Quality Scores

Gok M. Y., Sagiroglu M. S., ÜNSALAN C., Goren S.

21st Signal Processing and Communications Applications Conference (SIU), CYPRUS, 24 - 26 Nisan 2013, (Tam Metin Bildiri)

  • Yayın Türü: Bildiri / Tam Metin Bildiri
  • Doi Numarası: 10.1109/siu.2013.6531567
  • Basıldığı Ülke: CYPRUS
  • Anahtar Kelimeler: Bioinformatics, Field Progmammable Gate Array, Alignment, Hardware Alignment Quality Scores, SEQUENCES, DESIGNS, CELL
  • Marmara Üniversitesi Adresli: Hayır

Özet

Smith Waterman Algorithm is a widely used tool in bioinformatics to align reads from aligning to a reference in whole genome sequencing. Mapping millions of sequences read from sequencing is a computationally expensive operation. Accuracy and performance are two important aspects of this process. FPGA based solutions are widely studied. In this paper we tried to achieve a better mapping accuracy for optimum alignment using quality scores of the bases of read sequences while keeping the performance high. We are offering a new Smith Waterman processing unit and systolic array based on quality scores.