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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Accelerating the Next Generation Long Read Mapping with the FPGA-Based System
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Accelerating the Next Generation Long Read Mapping with the FPGA-Based System

机译：利用基于FPGA的系统加速下一代长时间读取映射

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摘要

To compare the newly determined sequences against the subject sequences stored in the databases is a critical job in the bioinformatics. Fortunately, recent survey reports that the state-of-the-art aligners are already fast enough to handle the ultra amount of short sequence reads in the reasonable time. However, for aligning the long sequence reads (>400 bp) generated by the next generation sequencing (NGS) technology, it is still quite inefficient with present aligners. Furthermore, the challenge becomes more and more serious as the lengths and the amounts of the sequence reads are both keeping increasing with the improvement of the sequencing technology. Thus, it is extremely urgent for the researchers to enhance the performance of the long read alignment. In this paper, we propose a novel FPGA-based system to improve the efficiency of the long read mapping. Compared to the state-of-the-art long read aligner BWA-SW, our accelerating platform could achieve a high performance with almost the same sensitivity. Experiments demonstrate that, for reads with lengths ranging from 512 up to 4,096 base pairs, the described system obtains a $10 times−48 times$ speedup for the bottleneck of the software. As to the whole mapping procedure, the FPGA-based platform could achieve a $1.8 times−3.3 times$ speedup versus the BWA-SW aligner, reducing the alignment cycles from weeks to days.
机译：将新确定的序列与数据库中存储的主题序列进行比较是生物信息学中的一项关键工作。幸运的是，最近的调查报告称，最先进的比对仪已经足够快，可以在合理的时间内处理大量的短序列读取。但是，对于比对下一代测序（NGS）技术产生的长序列读段（> 400 bp），使用现有比对器仍然效率不高。此外，随着测序技术的进步，随着序列读取的长度和数量都不断增加，挑战变得越来越严重。因此，对于研究人员来说，提高长读比对的性能非常迫切。在本文中，我们提出了一种新颖的基于FPGA的系统来提高长读映射的效率。与最先进的长读对准仪BWA-SW相比，我们的加速平台可以在几乎相同的灵敏度下实现高性能。实验表明，对于长度范围为512至4,096个碱基对的读取，所描述的系统获得的 $ 10乘以-48乘以$ 加快了软件瓶颈。对于整个映射过程，基于FPGA的平台可以实现 $ 1.8 times-3.3 times $ 加速与BWA-SW对准器相比，将对准周期从数周缩短至数天。

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