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Opportunity: Senior Bioinformatician @ Wellcome Trust Sanger Institute -- Hinxton/Cambridge, UK
Submitted by Sam Bowker; posted on Tuesday, July 8, 2014
OVERVIEW
Seeking an experience Senior Bioinformatician to develop new computational methods to use BWT reference-free structures to rapidly genotype newly sequenced human genomes.
The Sequence Variation Infrastructure team is involved in some of the largest human and mouse genome sequencing projects. In the coming years, we are interested in applying novel comparative genomics representations, such as BWT based compressed storage (1), HAL representation of multiple aligned genomes (2), and scalable noSQL key-value databases to make it possible to make very fast queries across thousands of human genomes.
We have recently applied these technologies in proof-of-principle datasets from the 1000 genomes project (3) and are now seeking an experienced Senior Bioinformatician or programmer to further develop methods to carry out carry out tasks such as rapid genotyping of newly sequenced human genomes for known SNPs, indels, and structural variants and to analyse across large volumes of sequencing data to contribute to answering specific scientific questions.
This role would suit somebody with some previous exposure to bioinformatics methods development or a scientific programmers with previous experience in a high performance computing environment who wishes to gain direct knowledge of next-generation sequencing technologies and analysis.
The successful candidate will work closely with two established teams of analysts and developers so previous experience with next-generation sequencing data is advantageous but not strictly necessary.
REQUIREMENTS
Essential Skills:
- A M.Sc. or Phd degree in a computational science (or equivalent industry experience)
- Evidence of proficiency in computer program design and implementation in a modern programming language (e.g. Perl, Java, C, C++, Python etc.)
- Ability to quickly adapt to new problems and ideas
- Excellent problem-solving skills
- Experience with managing large volumes of data
PREFERENCES
Ideal Skills:
- Experience with running software on a compute farm or cluster
- Experience of analysing data from multiple sequencing technologies
- Previous experience of developing computational methods to solve complex scientific problems
- Relational or noSQL database design and manipulation
- A high level of communication skills to be able to elicit complex requirements from, and convey complex information to, groups with different levels of technical knowledge
Other information
TERMS
Fixed-term for 3 years
COMPENSATION
Salary range: GBP 30196 to GBP 38088pa plus excellent benefits
Our Benefits include: Defined Benefit Pension Scheme, Group Income Protection, Healthcare scheme, Childcare Vouchers, Nursery and Annual Leave 25 days plus Bank Holidays.
ABOUT US
The Wellcome Trust Sanger Institute is a world leader in delivering large scale genome sequencing projects using the latest sequencing technologies. The Sequence Variation Infrastructure team work as part of the Computational Genomics programme with responsibility for development of highly used next-generation sequencing software packages (e.g. Samtools), development of systems to query across large volumes of sequencing data, are members of the Global Alliance for Genomics and Health (http://genomicsandhealth.org) data working group, and lead the Mouse Genomes Project (http://www.sanger.ac.uk/resources/mouse/genomes/). This project will be carried out in conjunction with the Vertebrate Resequencing Informatics team who are involved in data processing and analysis for several large human sequencing studies such as the 1000 Genomes, UK10K, and Haplotype Reference Consortium.
1. Simpson, J. T. et al. (2011) Genome Research, 22(3):549-56
2. Hickey, G. et al. (2013) Bioinformatics, 29:1341--1342
3. Liu, Zhicheng; McCarthy, Shane; Simpson, Jared; Iqbal, Zamin; Keane, Thomas; Durbin, Richard (2014): Using BWT structures for reference-free querying of the 1000 Genomes sequence data. figshare. http://dx.doi.org/10.6084/m9.figshare.108076)
The Genome Campus is a 100-acre estate south of Cambridge in the grounds of Hinxton Hall. Nestled in the quiet countryside of these landscaped gardens, are two world-class research facilities: the Wellcome Trust Sanger Institute and the European Bioinformatics Institute (EBI). The site has become the British hub of biomedical science. The Campus is also home to the Wellcome Trust Advanced Course and Scientific Conferences programme and the Wellcome Trust Conference Centre.
In addition to its peaceful location the campus offers excellent facilities including a start of the art data centre, gym, two cafes, a nursery, dining facilities, a cycle to work scheme, car sharing and free campus buses from various locations around Cambridge.
Learning, development and networking are other important aspects of life on campus. there are a range of scientific seminars with our own and invited speakers, scientific group meetings and skills development workshops.
DEADLINE
Closing date: 3rd August 2014
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