当前位置:
X-MOL 学术
›
arXiv.cs.AR
›
论文详情
Our official English website, www.x-mol.net, welcomes your
feedback! (Note: you will need to create a separate account there.)
A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing Applications on FPGAs
arXiv - CS - Hardware Architecture Pub Date : 2021-02-05 , DOI: arxiv-2102.03045 Nae-Chyun Chen, Yu-Cheng Li, Yi-Chang Lu
arXiv - CS - Hardware Architecture Pub Date : 2021-02-05 , DOI: arxiv-2102.03045 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.
中文翻译:
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。
更新日期:2021-02-08
中文翻译:
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。