QCKer-FPGA: An FPGA Implementation of Q- gram Counting Filter for DNA Sequence Alignment

摘要: Read mapping is a process in which DNA reads are mapped to reference genome through filtering and verification using predefined metric. Filtering done by quickly eliminating incorrect regions when read compared the genome. Verification on other hand responsible for verifying these candidate require mathematical theoretical approaches. Due large amounts of data produced Next Generation Sequencing (NGS) platforms, filter needed reduce various computational challenges introduced process. FPGAs special purpose processors that designed handle compute-intensive applications, having highly customizable fabric. In this paper, q-gram counting implemented takes advantage flexibility capabilities parallel applications ZedBoard development board. The paper discusses results with varying sizes q, number lengths, different sequences. show an average 34.02% lesser clock cycles length 4 53.58% 8 implementation C.