A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing Applications on FPGAs

Nae-Chyun Chen, Yu-Cheng Li, Yi-Chang Lu

FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level, raising a demand of an efficient algorithm for FM-index construction. In this work, we propose a hardware-compatible Self-Aided Incremental Indexing (SAII) algorithm and its hardware architecture. This novel algorithm builds FM-index with no memory overhead, and the hardware system for realizing the algorithm can be very compact. Parallel architecture and a special prefetch controller is designed to enhance computational efficiency. An SAII-based FM-index constructor is implemented on an Altera Stratix V FPGA board. The presented constructor can support DNA sequences of sizes up to 131,072-bp, which is enough for small-scale references and reads obtained from current major platforms. Because the proposed constructor needs very few hardware resource, it can be easily integrated into different hardware accelerators designed for FM-index-based applications.

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