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Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps
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DOI：10.1109/TCBB.2020.3000253.png)
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摘要
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The FM-index is a data structure used in genomics for exact search of input sequences over large reference genomes. Algorithms based on the FM-index show an irregular memory access pattern, resulting in a memory bound problem. We analyze a recent implementation of the FM-index and highlight existing throughput-memory trade-offs, showing that memory requirements limit implementation of large k-steps. We propose COFI, a COmpressed FM-Index for large K-steps. COFI enables a 15-step FM-index using less than 16 GB for a human genome reference of 3 giga base pairs. An algorithm based on this new layout is evaluated on both a Knights Landing (KNL) and an Skylake-based system (SKX). We achieve average speed-ups of 1.46x and 1.39x, respectively, with respect to an state-of-the-art FM-index implementation that is already well optimized.
Keyword:
Compressed FM-index
sequence alignment
knights-landing
skylake
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