Poretools: a toolkit for analyzing nanopore sequence data.
Poretools: a toolkit for analyzing nanopore sequence data.
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DOI：
10.1093/bioinformatics/btu555
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发表时间：
2014-12-01
期刊：
影响因子：
--
通讯作者：
Quinlan AR
中科院分区：
文献类型：
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作者：
Loman NJ;Quinlan AR
动机：纳米孔测序可能是基因组学中的下一个颠覆性技术，因为它能够在没有事先扩增的情况下检测单个DNA分子，不依赖昂贵的光学组件，并且能够对长片段进行测序。来自Oxford Nanopore Technologies（ONT）的MinION™是第一个商业化的纳米孔测序仪，现在可供早期访问用户使用。MinION™是一种USB连接的便携式纳米孔测序仪，允许实时分析流式事件数据。目前，研究界缺乏用于分析纳米孔数据集的标准化工具包。结果如下：我们引入了poretools，这是一种灵活的工具包，用于探索MinION™纳米孔测序设备生成的数据集，以进行质量控制和下游分析。Poretools直接在ONT生成的本地FAST 5（HDF 5标准的应用程序）文件格式上运行，并提供了丰富的格式转换实用程序以及数据探索和可视化工具。可用性和实施：Poretools是一个开源软件，用Python编写，既是一套命令行实用程序，也是一个Python应用程序编程接口。源代码可以在Github上免费获得，网址是https://www.github.com/arq5x/poretools联系人：n. j. bham.ac.uk和aaronquinlan@gmail.com补充信息：Github中有一个演示poretools功能的IPython笔记本。完整的文档可在http://poretools.readthedocs.org上获得。
Motivation: Nanopore sequencing may be the next disruptive technology in genomics, owing to its ability to detect single DNA molecules without prior amplification, lack of reliance on expensive optical components, and the ability to sequence long fragments. The MinION™ from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialized and is now available to early-access users. The MinION™ is a USB-connected, portable nanopore sequencer that permits real-time analysis of streaming event data. Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets. Results: We introduce poretools, a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION™ for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (an application of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. Availability and implementation: Poretools is an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code is freely available in Github at https://www.github.com/arq5x/poretools Contact: n.j.loman@bham.ac.uk and aaronquinlan@gmail.com Supplementary information: An IPython notebook demonstrating the functionality of poretools is in Github. Complete documentation is available at http://poretools.readthedocs.org.
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup