Problem
Research questions and friction points this paper is trying to address.
genomic analysis
data movement bottleneck
data preparation bottleneck
compressed storage
Storage-Centric System Designs for Enabling Fast, Efficient, and Low-Cost Genomic and Metagenomic Analyses
🤖 AI Summary
本文针对基因组和宏基因组分析中数据移动和准备的瓶颈问题，提出了一种以存储为中心的设计方案，通过在存储系统内部进行数据分析并支持高度压缩的数据存储，从而提高性能、能效及成本效益。
📝 Abstract
Genomic and metagenomic analyses play critical roles in many fields, such as precision medicine, urgent clinical settings, discovering early warnings of communicable diseases, ensuring food safety through pathogen monitoring, agriculture, and scientific discovery. Due to the challenges of analyzing and storing massive volumes of genomic and metagenomic sequence data, significant efforts have been made to accelerate (meta)genomic analyses and store sequence data compressed. Despite the benefits of these techniques, we identify two major outstanding problems in accessing stored sequence data and supplying it to the analysis units: (i) the data movement bottleneck due to moving large amounts of low-reuse data from storage and the unnecessary burden on the rest of the system, and (ii) the data preparation bottleneck, where compressed sequence data needs to be first decompressed and formatted before analysis.
In this dissertation, we present customized storage-centric systems, which efficiently (i) analyze (meta)genomic data inside the storage system, and (ii) enable highly-compressed storage and high-performance access of large-scale sequence data, thereby alleviating the overheads of data movement, computation, and data preparation. We demonstrate that the proposed systems significantly improve system performance, energy efficiency, and system cost-efficiency of (meta)genomic analysis. We hope that the storage-centric systems proposed in this dissertation facilitate the broader adoption of (meta)genomic analyses and inspire future research to fundamentally improve the performance, energy efficiency, and cost-effectiveness of other data-intensive application domains related to health and life sciences.
Innovation
Methods, ideas, or system contributions that make the work stand out.
storage-centric systems
data movement bottleneck
highly-compressed storage
high-performance access
energy efficiency
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