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Exploiting Nanopore sequencing for genome sequencing

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

We are exploiting the latest generation Nanopore sequencing approaches to sequence large genomes. Nanopore sequencing is low cost, easy to use and can generate read lengths limited only by the ability to generate suitable input material. The project will focus on developing methods to obtain high quality high molecular weight DNA to maximise read length on this platform. We are specifically interested in capturing genome data from species which provide inherent challenges to short read sequencing due to the presence of large repeats or other complex challenges. These data will be combined with those we have already generated to understand fundamental questions addressing the rates of change of genomes and gene gain/loss (see Evans et al 2014). Alongside this, the project will develop and exploit methods for selective sequencing on the minION – so called ’Read Until’ (See Loose et al 2016). We are world leaders in this approach, enabling the ‘tasting’ of reads in the sequencer in real time and the selective rejection of material that has been seen before or does not meet some other experimental criterion. We will investigate how ‘Read Until’ can be used to iteratively improve assemblies and guide sequencing in real time. The ease of sequencing is such that applicants are encouraged from a diversity of backgrounds including Biology, Physics, Mathematics or Bioinformatics.

The University of Nottingham is one of the world’s most respected research-intensive universities, ranked 8th in the UK for research power (REF 2014). Students studying in the School of Life Sciences will have the opportunity to thrive in a vibrant, multidisciplinary environment, with expert supervision from leaders in their field, state-of-the-art facilities and strong links with industry. Students are closely monitored in terms of their personal and professional progression throughout their study period and are assigned academic mentors in addition to their supervisory team. The School provides structured training as a fundamental part of postgraduate personal development and our training programme enables students to develop skills across the four domains of the Vitae Researcher Development Framework (RDF). During their studies, students will also have the opportunity to attend and present at conferences around the world. The School puts strong emphasis on the promotion of postgraduate research with a 2-day annual PhD research symposium attended by all students, plus academic staff and invited speakers.

Funding Notes

Home applicants should contact the supervisor to determine the current funding status for this project. EU applicants should visit the Graduate School webpages for information on specific EU scholarships View Website. International applicants should visit our International Research Scholarships page for information regarding fees and funding at the University View Website.

References

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.
The potential impact of nanopore sequencing on human genetics.
Loose MW.
Hum Mol Genet. 2017 Oct 1;26(R2):R202-R207. doi: 10.1093/hmg/ddx287. Review.

Real-time selective sequencing using nanopore technology.
Loose M, Malla S, Stout M.
Nat Methods. 2016 Sep;13(9):751-4. doi: 10.1038/nmeth.3930. Epub 2016 Jul 25.
Acquisition of germ plasm accelerates vertebrate evolution.
Evans T, Wade CM, Chapman FA, Johnson AD, Loose M.
Science. 2014 Apr 11;344(6180):200-3. doi: 10.1126/science.1249325.

How good is research at University of Nottingham in Biological Sciences?

FTE Category A staff submitted: 90.86

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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