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FM-index is an efficient data structure for string search and is widely usedin next-generation sequencing (NGS) applications such as sequence alignment andde novo assembly. Recently, FM-indexing is even performed down to the readlevel, raising a demand of an efficient algorithm for FM-index construction. Inthis work, we propose a hardware-compatible Self-Aided Incremental Indexing(SAII) algorithm and its hardware architecture. This novel algorithm buildsFM-index with no memory overhead, and the hardware system for realizing thealgorithm can be very compact. Parallel architecture and a special prefetchcontroller is designed to enhance computational efficiency. An SAII-basedFM-index constructor is implemented on an Altera Stratix V FPGA board. Thepresented constructor can support DNA sequences of sizes up to 131,072-bp,which is enough for small-scale references and reads obtained from currentmajor platforms. Because the proposed constructor needs very few hardwareresource, it can be easily integrated into different hardware acceleratorsdesigned for FM-index-based applications.

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