The Pirbright Institute’s Bioinformatics, Sequencing, and Proteomics group combines advanced genomics and bioinformatics to support high-impact research.
We offer cutting-edge sequencing and analysis within high-containment environments, utilising technologies like Illumina and Oxford Nanopore, and develop specialized tools to drive innovations in animal virology.
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 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 unit's bioinformatic activities focus on the development and delivery of robust and highly sensitive analysis pipelines for 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.
Specialist equipment
The facility houses:
- Hamilton Microlab-STAR Sequencers
- Illumina MiSeq
- NextSeq-550, iSeq-100
- 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.
Team
Dr Graham Freimanis, Scientist. Sequencing Lead
Dr Tim Downing, Group Leader, Bioinformatics
Dr Nicos Angelopoulos, Group Leader, Bioinformatics core co-lead
Noemi Polo, Research Technician, Sequencing
Dr Chandana Tennakoon, Senior Bioinformatician, Bioinformatics core
Lily Yang, Senior Bioinformatician, Bioinformatics core
Contact
Services are available for internal/collaborative use only.
Access to unit resources can be granted by contacting the team members above.
