Preface content

Bioinformatics and sequencing in high-containment

About

Genomics technologies, in particular high-throughput sequencing and bioinformatics have revolutionised modern biology and genetics.  As a result, building capability in both areas is a critical strategic priority for the Institute, necessary to underpin the high-quality research described in both Pirbright’s Host and Virus research programmes.  To achieve this, we have unified bioinformatics and high-throughput sequencing activities under a single unit – the Bioinformatics, Sequencing and Proteomics group.  This coordinated approach will enable us to get the best from both worlds through the production of pipelines spanning ‘from sample to data’: tailored sequencing protocols that provide high quality data for subsequent cutting-edge bioinformatics analysis, again specifically addressing project goals.

High-throughput sequencing

We provide a unique sequencing solution within high containment, with world class facilities.  As work at the institute involves a number of SAPO4 viral agents that are unable to leave the containment envelope, this arrangement offers us the invaluable and unprecedented opportunity to perform cutting-edge research on these agents in situ.

Current facilities are mostly built around the Illumina technology platform, but we are also exploring novel technologies providing longer reads, such as the Oxford Nanopore MinION.

We have several Illumina sequencers, each tailored to different output scales and specifications.  They provide established workflows for genetics, transcriptomics and epigenetics, as per the Institute’s research programmes.  Our DNA- and RNA-sequencing capabilities allow us to deploy core workflows that include whole genome sequencing, targeted amplicon, RNA and PCR-free applications.  We collaborate closely with others at the Institute in the provision of training and resources for researchers to learn and perform library preparation in a dedicated ‘clean’ environment within the SAPO4 envelope.

As part of our key goals we have automated core sequencing pipelines using a Hamilton NGS Star, in order to standardise high quality sequencing library production.  Dedicated staff within the unit have extensive experience in a wide range of protocols (including RNA-seq, miRNA-seq and ribosome profiling) and can develop bespoke processes that cannot be supported by established high throughput sequencing pipelines.  This is an important part of our strategy as we seek to maximise the sequencing potential across the diverse and important historical sample archives held within the Institute.

Another strength in our strategy is the emphasis on embracing novel and emerging genomics methodologies, ensuring science at Pirbright remains at the cutting edge of animal virology science. In line with this we are working to establish a strong single cell capability within the Institute and have recently procured a Dolomite Bio micro-encapsulator and a 10X Chromium sited within the Gates Hub.  This new equipment will enable the deployment of droplet-based protocols, including single cell transcriptomics, (Drop-seq) and immunological profiling.    

Bioinformatics

The units bioinformatic activities focus on the development and delivery of robust and highly sensitive analysis pipelines for the de-novo assembly of DNA/RNA viruses, RNA-sequencing analysis and tools aimed at the evolutionary analysis of viral/host sequences.  These novel in-house pipelines have already been applied to a number of Pirbright projects including the characterisation of FMDV quasi-species in buffalo, the genomic analysis of vector species and the determination of biomarkers in Marek’s disease virus infection.

We are also committed to developing specialist tools, such as variant callers specialised for viral data and integrative tools to analyse data deriving from a combination of protocols and conditions.

The group also run Pirbright’s high performance computing cluster. With ~1000 hyper-threaded CPU cores, 4TB RAM and 0.5 PB of storage, it provides quantitative scientists at the Institute with a modern cutting-edge high speed data analysis capability.

History

The resource was officially established and funded in November 2017.

Specialist equipment

Bioinformatics_Hamilton ML STAR_001
An image of the new robotic capability - the Hamilton Microlab-STAR
Sequencers within high containment include an Illumina MiSeq, NextSeq-550, iSeq-100 and Oxford Nanopore MinION.  We have integrated these systems in with lab-based automation with a Hamilton ML-STAR.  For single cell investigations and other droplet-based applications we have a Dolomite Bio microencapsulator.

Bioinformatics capabilities include the high performance computing cluster.

Services offered

Internal/collaborative only.  Please contact the team for further information. 

Booking the facility

Access to unit resources can be granted by contacting the team members below. 

Resources links, tools or downloads

Please see the Integrative Biology group for further information.

The team


Dr Graham Freimanis, Scientist. Sequencing Lead
Dr Chandana Tennakoon, Scientist, Bioinformatician
Dr Adrian Silesian, Scientist, Bioinformatician 

Contact

For further information please contact Dr Graham Freimanis or Dr Chandana Tennakoon:
The Pirbright Institute
Ash Road
Pirbright
GU24 0NF

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