Mitigating memory latency in FM Index search

Bowtie 2 is a popular short sequence aligner used by many bioinformatics groups, often as part of the Qiita microbial study management platform. One of the key computational steps during alignment is the extraction of seeds from the read sequences and aligning them with the help of the FM Index. This step was memory access-bound, with access latency as the primary limitation due to a pseudo-random-access pattern. In this paper we present the algorithmic changes used and the performance improvements obtained by re-factoring the code to overlap compute with memory pre-fetching.