Finding maximal exact matches (MEMs) is an important building block of many workloads including genome alignment.
Hence its acceleration has a great impact on genome alignment and genome analysis workloads.
In this paper, we developed a new algorithm, FBWTMEM, for this task, and experimentally showed that our algorithm outperforms previous ones.
We achieved 1) a smaller memory footprint by using a recently-proposed data structure called FBWT and 2) a faster execution time by adaptively tuning the skip parameter.
By: Masaru Ito, Hiroshi Inoue, Megumi Ito and Moriyoshi Ohara
Published in: RT0981 in 2017
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