k-Core: Hardware Accelerator for k-Mer Generation and Counting used in Computational Genomics

摘要

In computational genomics, the term k-mer typically refers to all the possible subsequences of length k from a single read obtained through DNA sequencing. In genome assembly, generating frequency of k-mers takes the highest compute time. k-mer counting is considered as one of the important analyses and the first step in sequencing experiments. Here, we present an FPGA based fast k-mer generator and counter, k-core to generate unique k-mers and count their frequency of occurrence. The IP core is parameterizable in terms of the line length (l) and k-mer size (k) and is implemented on XCVU095 FPGA. A speed up of about 6.6×, 5.46× and 8.5×, are achieved compared to [1], [2], [3] CPU implementations respectively and about 5.26× with respect to [1]'s GPU version.