Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices
Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices
复制标题
识别移动设备上宏基因组 DNA 流中的分类单元
DOI：
10.1109/tcbb.2022.3172661
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Zola, Jaroslaw
中科院分区：
文献类型：
--
作者：
Zheng, Vicky;Sariyuce, A. Erdem;Zola, Jaroslaw
随着便携式DNA测序仪（如Oxford Nanopore Technology MinION）的出现，宏基因组DNA测序可以实时、直接地在现场进行。然而，由于宏基因组DNA分析任务，如分类、分类单位分配等，需要大量的计算和内存，而且现有的方法是为批量处理而设计的，目前的宏基因组工具不太适合移动设备。在这项工作中，我们提出了一种新的记忆效率方法来识别移动设备上宏基因组DNA流中的操作分类单元（otu）。我们的方法是基于在MinION平台生成的实时长DNA读取流上构建的重叠图中找到连接的组件。我们提出了一种有效的算法来保持重叠图的连接组件，并展示了如何通过传递闭包从流中删除冗余信息。我们还提出了如何将我们的算法集成到为移动计算量身定制的更大的DNA分析管道中。通过在实际移动设备上执行的模拟和真实宏基因组数据实验，我们证明了我们的解决方案能够高精度地恢复otu。我们的实验也证明了在DNA分析管道中引入反馈回路的复合效益。
With the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagenomic DNA analysis tasks, e.g., classification, taxonomic units assignment, etc., are compute and memory intensive, and the available methods are designed for batch processing, the current metagenomic tools are not well suited for mobile devices. In this work, we propose a new memory-efficient approach to identify Operational Taxonomic Units (OTUs) in metagenomic DNA streams on mobile devices. Our method is based on finding connected components in overlap graphs constructed over a real-time stream of long DNA reads as produced by the MinION platform. We propose an efficient algorithm to maintain connected components when an overlap graph is streamed and show how redundant information can be removed from the stream by transitive closures. We also propose how our algorithms can be integrated into a larger DNA analysis pipeline tailored for mobile computing. Through experiments on simulated and real-world metagenomic data, executed on the actual mobile device, we demonstrate that our resulting solution is able to recover OTUs with high precision. Our experiments also demonstrate the compounding benefits of introducing feedback loops in the DNA analysis pipeline.
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影响因子：
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DOI：
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发表时间：
2006
期刊：
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DOI：
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发表时间：
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期刊：
bioRxiv
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DOI：
10.1007/978-3-642-19754-3_20
发表时间：
2011
期刊：
European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery
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DOI：
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发表时间：
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期刊：
SC15: International Conference for High Performance Computing, Networking, Storage and Analysis
影响因子：
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作者：
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