DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer's ionic current signal. We map three cytosine variants and two adenine variants.
Mobile/portable (third-generation) sequencing technologies, including Oxford Nanopore’s MinION and SmidgION, are revolutionizing once again –after the advent of high-throughput sequencing– biomedical sciences.
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software.
The recent launch of the Oxford Nanopore Technologies MinION Access Program (MAP) resulted in the rapid development of a number of open source tools aimed at extracting reads and yield information from the HDF5 format files produced by the platform.
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost.
The enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions.
The MinION replaces the conventional model of "sequence followed by analysis to final result" with instant access to data before the completion of a sequencing run. This instant access extends to the analysis of sequence "squiggle" data even before a read has finished traversing the nanopore.
The Applications team at Oxford Nanopore has two overarching responsibilities: creation and development of sample and library preparation protocols for a wide variety of sample types, and undertaking biological projects which highlight the various strengths of Oxford Nanopore’s technology.
Clinical pathogen sequencing has been demonstrated to have a positive outcome on treatment of patients with unknown bacterial infection. However, widespread adoption of clinical pathogen sequencing has been impeded by the lack of real-time sequencing devices.
Nanopore sequencing introduces true real-time sequencing for the first time. Full exploitation of real-time sequencing requires a novel approach to data analysis for which we have developed the minoTour platform.
In my talk, I will discuss my collaboration with Nick Loman’s lab to develop de novo assembly methods for MinION data. We have built a pipeline to error correct nanopore reads using partial order graphs and the corrected reads are subsequently assembled using the Celera Assembler.
We report a rapid, inexpensive, and portable strategy to re-identify human DNA using the MinION, a miniature sequencing sensor by Oxford Nanopore Technologies. Our strategy requires only 10-30 minutes of MinION sequencing, works with low input DNA, and enables familial searches.
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate.