QCKer: An x86-AVX/AVX2 implementation of Q-gram counting filter for DNA sequence alignment

• Main Authors: Pernez, Joven L., Uy, Roger Luis, Borja, Kaizen Vinz A., Maghirang, Jan Carlo G.
• Format: text
• Published: Animo Repository 2019
• Subjects: Simultaneous multithreading processors; Nucleotide sequence; Gene mapping; Computer Sciences
• Online Access: https://animorepository.dlsu.edu.ph/faculty_research/4037
• Institution: De La Salle University

The paper presents the implementation of the q-gram counting filter using x86-AVX/AVX2 SIMD instructions. There are three novel findings during the course of the research work. First, to eliminate inconsistency between the theoretical and experimental result, synthetic reads are generated using DNA...