Exact Alignment with FM-Index on the Intel Xeon Phi Knights Landing Processor

The FM-index is an efficient data structure useful for searching strings in large reference texts. In fact, FMindex is used in many sequence aligner tools. Due to the data structure layout, the searching process based on FM-index exhibits irregular memory access patterns, causing a high cache miss rate. Besides, it is common for the search algorithm to be memory bound due to the low arithmetic intensity. As a result, different versions of FM-index and corresponding aligning algorithms were designed to minimize memory traffic due to those random accesses. This paper describes various aligning algorithms based on FM-index and propose a modification of the FMindex data structure capable of reducing memory bandwidth and increase operational intensity, in order to attain a performance near the limit given by the peak random access memory bandwidth. Experiments on a Xeon Phi KNL processor obtain a throughput (Lastto-First operations per second) much higher than GPU and CPU implementations previously reported in the literature.