NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing
Scientists at TGAC have been putting Oxford Nanopore’s MinION sequencer through its paces with an open-source, sequence alignment-based genome analysis tool called ‘NanoOK’.
NanoOK is the first open-source tool that provides comprehensive alignment-based quality control and error profile analysis for the MinION platform. NanoOK’s main output is a detailed PDF report featuring graphs and tables of sample analysis data. Individual graphs are also available to include in publications and presentations and the raw data is available for users to perform additional custom analysis.
The tool currently supports four popular Nanopore aligners but is easily extensible through a Java programming interface. It also handles metagenomic sampling gracefully, due to support for multiple reference sequences and the output report PDF benefits from programming language R’s graphical capabilities, for at-a-glance reporting of large data volumes.
The MinION is a compact, portable device, smaller than a typical TV remote control and produces long reads in the kilobase length range. A USB-connected device, its compact size and portability makes it ideal for low-cost research fieldwork. NanoOK’s comprehensive alignment-based error profiling enables researchers to understand data quality, the effect of different alignment tools and to understand the effect of updates to the MinION’s chemistry and software.
Lead author Dr Richard Leggett, Project Leader in the Data Infrastructure & Algorithms Group at TGAC, said: “The speed of change within the MinIon Access Programme (MAP) is rapid and a tool such as NanoOK can help researchers to understand and evaluate changes. This will be crucial as anticipated updates are rolled out, such as the ‘fast run mode’ announced at Oxford Nanopore’s May London Calling event.”
“NanoOK provides comprehensive alignment-based analysis of Nanopore reads through a simple, easy to use interface. During our progress through the MAP, we have found it to be an invaluable tool for understanding the data emerging from the sequencer and we believe it will have wide applicability to other groups working with the MinION.”
The paper, titled: NanoOK: "Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles" is published in Bioinformatics.
TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
NanoOK is open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded here. A VirtualBox VM containing all dependencies and the DH10B read set used in the paper is available here.
The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology. TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) - £7.4M in 2013/14 - as well as support from other research funders. TGAC is one of eight institutes that receive strategic funding from BBSRC. TGAC operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
TGAC offers state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a Training programme through courses and workshops, and an Outreach programme targeting schools, teachers and the general public through dialogue and science communication activities. www.tgac.ac.uk
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, and with an annual budget of around £467M (2012-2013), we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.