BBSRC iCASE PhD studentship: Real Time Nanopore Sequencing at Scale – Read Until and Run Until on PromethION scale devices

Rapid sequencing transforms our understanding of the biological world. New technologies provide new challenges developing optimal approaches to address biological questions. Oxford Nanopore Technologies (ONT) enable real time sequencing as sequence data can be analysed during data generation. We exploited this technology in a number of ways, establishing “read until”. The read start is analysed whilst being sequenced. If this matches a region of interest, sequencing can continue. If not the read can be rejected and another sequenced. This enables selective sequencing of specific molecules from a library. We first demonstrated this method works using dynamic time warping to map nanopore signal to a reference. Subsequently, we have jointly developed an approach to basecall sequence data directly from the squiggle trace whilst sequencing.

This method removes limitations of searching within signals and can be used by all with the same hardware. The method is limited presently to the GridION and MinION. These can generate 10-20 Gb of data per flowcell. The PromethION sequencer generates in excess of 100 Gb of sequence data per flowcell from 48 positions simultaneously. This enables human genome sequencing within 60 hours on a single flowcell with long reads. Selective sequencing at scale enables useful applications such as a low coverage whole genome coupled with higher coverage specific regions e.g cancer-causing SNPs or structural variants of interest.

“Read Until” impacts flowcell performance and requires optimisation depending on experimental goal. Working with ONT to determine the underlying reasons for this we will develop methods to implement “Read Until” on PromethION including: Run Until automatically stopping sequencing once a specific experimental goal is achieved and coupling this with ‘read until’ enabling reads to be rejected which are no longer required. Methods will include genome assembly, targeted coverage of regions of whole genomes, and filtering of metagenomes. We will also establish methods exploiting one or more sequencing positions simultaneously. These methods will be dynamic, offering flexibility over and above custom library preparation enriching for specific targets.

Entry Requirements
Applicants should have, or expect to achieve, at least a 2:1 Honours degree (or equivalent).

Studentship information
It is fully funded for four years. The award would be fees (£4409 p.a.) plus an annual stipend (£15,285 p.a. for Oct 2020), set by the Research Councils.

How to apply
The 4-year PhD studentship will be filled as soon as a suitable candidate has been found, candidates are therefore encouraged to apply via https://www.nottingham.ac.uk/bbdtp/apply/apply-online.aspx as soon as possible.

Prospective applicants are encouraged to contact [Email Address Removed] for more details about the project or visiting https://www.nottingham.ac.uk/bbdtp/case-2020/case-2020.aspx

Closing date: noon, Tuesday 14th July 2020.

The start date is 1 October 2020.

Eligibility
This fully-funded studentship is available to UK students and EU students who have lived in the UK for 3 years prior to the start of their studies. EU students without meeting this criteria are eligible for a fees-only award.