minoTour: A real time analysis and data management platform for Oxford Nanopore minION reads.

minoTour：Oxford Nanopore minION 读取的实时分析和数据管理平台。

• 批准号: BB/M020061/1
• 负责人: Matthew Loose
• 金额: $ 18.83万
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM020061%2F1
• 关键词: minoTour; real; time; analysis; data

The last 15 years has seen a dramatic explosion in the impact that DNA sequencing has had on our lives. From the announcement of the first draft human genome sequence in 2000 at an estimated cost of $2.7 billion to the announcement of the $1000 genome in 2014, the rate of growth in sequencing technology has been exponential. The main drive behind the dramatic lowering in cost is the development of massively parallel short read sequencing technologies from companies such as Illumina. These approaches generate short fragments of sequence, typically 75 - 300 base pairs in length, from the material being sequenced which are subsequently combined computationally to reassemble the original sequence. These approaches have generated vast quantities of data and revealed much that we did not know about biology. The establishment of long read sequencing platforms, first developed by PacBio, once again hold the potential for a step change in sequencing technologies. In particular, the portable nanopore based sequencer, minION, developed by Oxford Nanopore Technologies represents a significant new technology. In contrast with previous technologies, sequence reads are generated in almost real-time. As these reads can be very long they can provide information about the material being sequenced almost immediately. Currently no tools exist which truly exploit these real-time features. We are participating in the minION access program and have developed the first real-time analysis platform, as a proof of principle, called minoTour. This suite of tools aims to rapidly identify DNA sequences as they are generated and report the results back to the experimentalist via a simple web-based interface. Key components include sending notifications to an experimentalist in real-time as events take place. For example the detection of a sequence from a specific pathogen or achieving enough sequence coverage to recognise key events from sequence data. The key advantages of a web-based interface to such a platform are ease of use for an experimentalist in a wide variety of environments. Currently the minION platform requires an always on connection to the web for generation of the sequence data. In the future it is anticipated that this technology will be available on the local machine. The tools we are developing will also be able to run without a network connection allowing experimentalists to sequence and analyse data in the field. A broader extension of our approach focusses on de novo assembly of sequence data as it is generated. Early results suggest that de novo assembly from minION data is possible and this would allow for another broad range of applications both in the laboratory and the field. In the future tools such as the minION will be developed as basic sensing devices used in a number of different environments. Having real-time access to the data they generate in a manner similar to that proposed here would allow for the rapid detection of contaminants in a wide range of environments. Similarly it is easy to imagine the lab scientist wishing to sequence a DNA construct having their results within 30 minutes, representing significant savings in time and effort for a large number of projects.

在过去的15年里，DNA测序对我们生活的影响发生了戏剧性的爆炸。从2000年宣布第一个人类基因组序列草案，估计成本为27亿美元，到2014年宣布1000美元的基因组，测序技术的增长速度呈指数级。成本大幅降低背后的主要驱动力是Illumina等公司开发的大规模并行短读段测序技术。这些方法从被测序的材料产生短的序列片段，通常长度为75 - 300个碱基对，其随后通过计算组合以重组原始序列。这些方法产生了大量的数据，揭示了许多我们不知道的生物学知识。首先由PacBio开发的长读段测序平台的建立，再次为测序技术的一步变革带来了潜力。特别是，由Oxford Nanopore Technologies开发的便携式基于纳米孔的测序仪minION代表了一种重要的新技术。与以前的技术相比，序列读取几乎是实时生成的。由于这些读段可以非常长，它们几乎可以立即提供关于被测序的材料的信息。目前还没有真正利用这些实时功能的工具。我们参与了minION访问计划，并开发了第一个实时分析平台，作为原理证明，称为minoTour。这套工具旨在快速识别DNA序列，并通过一个简单的基于网络的界面将结果报告给实验者。关键组件包括在事件发生时实时向实验者发送通知。例如，检测来自特定病原体的序列或实现足够的序列覆盖以从序列数据中识别关键事件。基于网络的界面的主要优点是这样一个平台的实验在各种环境中易于使用。目前，minION平台需要始终连接到Web以生成序列数据。预计未来该技术将在本地计算机上可用。我们正在开发的工具也将能够在没有网络连接的情况下运行，允许实验人员在现场对数据进行排序和分析。我们的方法的更广泛的扩展集中在从头组装的序列数据，因为它是生成的。早期的结果表明，从头组装minION数据是可能的，这将允许在实验室和现场的另一个广泛的应用。在未来，诸如minION之类的工具将被开发为在许多不同环境中使用的基本传感设备。以类似于这里提出的方式实时访问它们生成的数据将允许在广泛的环境中快速检测污染物。同样，很容易想象实验室科学家希望在30分钟内测序DNA构建体，这代表了大量项目的时间和精力的显着节省。

项目成果

MinION Analysis and Reference Consortium: Phase 1 data release and analysis.

• DOI: 10.12688/f1000research.7201.1
• 发表时间: 2015
• 期刊: F1000Research
• 作者: Ip CLC;Loose M;Tyson JR;de Cesare M;Brown BL;Jain M;Leggett RM;Eccles DA;Zalunin V;Urban JM;Piazza P;Bowden RJ;Paten B;Mwaigwisya S;Batty EM;Simpson JT;Snutch TP;Birney E;Buck D;Goodwin S;Jansen HJ;O'Grady J;Olsen HE;MinION Analysis and Reference Consortium
• 通讯作者: MinION Analysis and Reference Consortium

Real-time selective sequencing using nanopore technology.

• DOI: 10.1038/nmeth.3930
• 发表时间: 2016-09
• 期刊: NATURE METHODS
• 影响因子: 48
• 作者: Loose, Matthew;Malla, Sunir;Stout, Michael
• 通讯作者: Stout, Michael

AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts.

Alignwise：一种用于识别蛋白质编码序列和校正框架切换的工具。

• DOI: 10.1186/s12859-015-0813-8
• 发表时间: 2015-11-09
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Evans T;Loose M
• 通讯作者: Loose M

Real time selective sequencing using nanopore technology.

使用纳米孔技术的实时选择性测序。

• DOI: 10.1101/038760
• 发表时间: 2016
• 作者: Loose M

MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.

• DOI: 10.12688/f1000research.11354.1
• 发表时间: 2017
• 期刊: F1000Research
• 作者: Jain M;Tyson JR;Loose M;Ip CLC;Eccles DA;O'Grady J;Malla S;Leggett RM;Wallerman O;Jansen HJ;Zalunin V;Birney E;Brown BL;Snutch TP;Olsen HE;MinION Analysis and Reference Consortium
• 通讯作者: MinION Analysis and Reference Consortium