一种基于FPGA的下一代排序应用的内存高效FM索引构造器
A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing Applications on FPGAs
摘要：
FM-索引是用于字符串搜索的有效数据结构，并且广泛用于下一代测序（NGS）应用，例如序列比对和从头组装。最近，FM索引甚至被执行到读取级别，提高了对FM索引构建的有效算法的需求。在这项工作中，我们提出了一个硬件兼容的自辅助增量索引（SAII）算法和它的硬件架构。该算法在建立FM索引时不需要占用内存，而且实现算法的硬件系统非常紧凑。为了提高计算效率，设计了并行结构和专用的预取控制器。基于SAII的FM索引构造器在Altera Stratix V FPGA板上实现。所呈现的构造器可以支持大小高达131，072-bp的DNA序列，这对于从当前主要平台获得的小规模参考和读取是足够的。由于所提出的构造器需要很少的硬件资源，它可以很容易地集成到不同的硬件加速器设计的FM索引为基础的应用程序。
英文摘要：
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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