UEA MED Genomic Pipelines

At UEA MED genomics we specialise in the analysis of high-throughput genomics and sequencing data. Our facility is based at the Bob Champion Research and Education Building (BCRE) within the Norwich Research Park. MED genomics provides a new service funded by UEA MED to facilitate analysis of complex sequencing datasets to aid ongoing and high impact research.

We have developed pipelines that automate the essential steps for processing sequencing samples and that produce a user-friendly report to summarise results. All samples undergo a rigorous quality control (QC) pipeline that including FastQC and Picard tools prior to the main analysis. For DNA-sequencing, we accept both exome and whole-genome samples for the analysis of germline or somatic variants. These pipelines incorporate other well-established pipelines developed at the Sanger Institute (cgpMAP, cgpWXS and cgpWGS) in addition to pipelines we have developed in-house, utilising other popular variant analysis tools (e.g. GATK and Freebayes).

Each pipeline produces a HTML report that includes interactive tables and graphs to summarise results. Further explanation of our pipelines can be found in our pipelines section and examples of our previous projects and reports in the projects section. In addition to our current pipelines, we also offer bespoke analyses upon request. For further information of this service please use the contact tab to email us directly.

Available pipelines

September 2020

Germline variant caller

Our germline variant calling pipeline has been created in-house utilising Freebayes and the GATK rare variant discover workflow. We use this in combination with Ensembl’s variant effect predictor (VEP) and gnomAD to filter for rare and predicted deleterious variants.

September 2020

Somatic variant caller

Following the sample QC, our somatic pipeline can be performed on tumor-normal matched samples. Samples are analysed using Sanger’s variant pipelines for exome (cgpWXS) or whole-genome sequencing (cgpWGS) in addition our in-house pipeline that utlises Mutect2 and the GATK workflow tools.

September 2020

Variant QC Pipeline

We have developed quality control (QC) pipelines that automate a number of tools to ensure sample fidelity. This pipeline processes samples from RNA-seq and DNA-seq (exome and WGS) followed by mapping.

Pipelines in development

RNA-seq

We are currently developing our an RNA-seq pipeline that utilises the HISAT2 aligner and StringTie for differential expression analysis. Unsupervised hierachial clustering, gene expression heatmaps and gene-ontology analyses are also being intergrated as part of this pipeline. Like our other pipelines, a HTML report summarising results will be generated creating interactive tables and plots. For more information please contact us directly using the contact tab.

SEPATH

SEPATH provides a benchmarked and convenient approach to detect pathogens in tissue sequence data helping to determine the relationship between metagenomics and disease. For more information visit the SEPATH github here or contact us directly using the contact tab.

Projects

Cholesteatoma - rare variant discovery

Cholesteatoma is a rare disease that results in cyst-like growths in the inner ear. In order to gain further understanding into the aetiology of the disease, nine family’s exomes were sequenced. Here we show some of the analyses run as part of our germline variant discovery pipeline.

Colorectal cancer tumoroid project

This project utilised DNA-exome sequencing on colorectal tumoroid and normal organoid cultures grown in 3D culture and were analysed for somatic mutations to identify patient specific drug targets. Here we show some of the analyses run as part of our Exome and somatic variant discovery pipeline.

Training and consultation

Providing bioinformatics tools, analysis and advice for research

Our services

Pipeline development
Bioinformatics analysis
Training
Statistics
Consultancy

Expert advice and Training

At UEA-MED genomics we are experts in next generation sequencing and analysis and we are here to provide advice and if required training. We are experienced bioinformaticians and statisticians with a background in biology (see our team). We can offer one-to-one consulation to help you with your analysis needs. For more information please us the contact us using the form below.