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The OCMS supports the bioinformatics aspect of microbiome studies with our expertise in microbiome analysis and data interpretation. The centre has developed a number of computational pipelines that enable efficient and reproducible analyses of high-through put microbiome datasets. Our experience includes processing and analysis of 16S rRNA gene profiling and metagenomics analysis of various types of samples. Details on analysis methods and pipelines can be found on our github page and blog. 

As part of the Kennedy Institute of Rheumatology, the OCMS utilises a high-performance compute facility capable of storing and processing large datasets produced in microbiome studiesPart of the OCMS provision is access to this hardware and software via a dedicated bioinformatician capable of deriving important insights from complex datasets. 

The manner of bioinformatics support provided is flexible, based on individual projects’ needs, such as processing sequences to generate analysis-ready data or exploration of covariates and their associations with microbial profiles. We welcome consultation throughout your grant-writing process to advise on bioinformatic requirements on collaborative projects. Below is a general breakdown of the levels of bioinformatics support we provide, though the extent of bioinformatics support is always determined on a per-basis. 

 

Level 1: Basic 16S data processing 

  • Process raw sequences for quality 

  • Analyse positive and negative control 

  • Classify to genus level 

  • Provide counts and taxonomy tables 

 

Level 2: Hypothesis generating analysis 

  • Everything in Level 1 

  • Alpha and beta diversity 

  • Composition profiles and PCA 

  • Limited significance testing for purposes of generating hypotheses 

 

Level 3: Hypothesis testing analysis 

  • Everything in previous levels 

  • Modelling and significance testing for purposes of testing hypotheses 

  • Interpretation of results 

 

Level 4: Supervision 

  • Everything in Level 1 

  • Collaborator does analysis with on-going support from OCMS bioinformatician(s) 

 

  

Please contact us at ocms@kennedy.ox.ac.uk to enquire about our bioinformatics services. 

 

 

Bioinformatics