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.

中文翻译：

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FPGA上下一代测序应用的内存高效FM-Index构造器

FM-index是用于字符串搜索的有效数据结构，已广泛用于下一代测序（NGS）应用程序中，例如序列比对和从头组装。近来，FM索引甚至被执行到读取级别，从而提出了用于FM索引构建的有效算法的需求。在这项工作中，我们提出了一种与硬件兼容的自助式增量索引（SAII）算法及其硬件体系结构。这种新颖的算法无需存储开销即可构建FM索引，并且用于实现该算法的硬件系统可以非常紧凑。并行架构和特殊的预取控制器旨在提高计算效率。基于SAII的FM-index构造函数在Altera Stratix V FPGA板上实现。提出的构建子可以支持最大131,072-bp的DNA序列，这对于从当前主要平台获得的小规模引用和读取就足够了。由于建议的构造函数需要很少的硬件资源，因此可以轻松地将其集成到为基于FM索引的应用程序设计的不同硬件加速器中。