Programmable Hardware based Short Read Aligner Using Phred Quality Scores
ASE/IEEE International Conference on Social Computing (SocialCom), Washington, Kiribati, 8 - 14 Eylül 2013, ss.864-867, (Tam Metin Bildiri)
- Yayın Türü: Bildiri / Tam Metin Bildiri
- Doi Numarası: 10.1109/socialcom.2013.130
- Basıldığı Şehir: Washington
- Basıldığı Ülke: Kiribati
- Sayfa Sayıları: ss.864-867
- Anahtar Kelimeler: genome mapping, alignment, FPGA, Phred, short read, hardware alignment, DESIGNS
- Marmara Üniversitesi Adresli: Hayır
Özet
Smith Waterman Algorithm is a widely used tool in bioinformatics. It aligns reads to a reference in whole genome sequencing. Mapping millions of sequences reads to a reference is a computationally expensive operation. Here, accuracy and performance are two important aspects of the process. Therefore, FPGA based solutions are widely used for this problem. In this study, we try to achieve a better mapping accuracy to achieve optimum alignment using Phred Quality scores of the bases of read sequences while keeping the performance high. We offer a new Smith Waterman processing unit and systolic array based on quality scores.