Project properties
Title Merging of amplicon and metagenomics data for sequencing data from the piglet gut microbiome.
Group Systems and Synthetic Biology
Project type thesis
Credits 36
Supervisor(s) Dr Jasper Koehorst; Mike Loomans
Examiner(s) Dr Jasper Koehorst
Contact info robert1.smith@wur.nl
Begin date 2024/04/18
End date
Description The public domain contains many pig gut microbiome datasets (ENA), most of which are amplicon data, this contrasts with the data that will be generated which will be shotgun metagenomics data. Applying conclusions drawn from amplicon studies directly to metagenomics data would initially require scepticism on the part of the reader as a meta-analysis between metagenomic and amplicon studies concerning pig data is absent. The student will work on creating an approach that integrates amplicon sequencing with metagenomic shotgun sequencing across techniques. The methods described by Usyk, et al. mention a framework for comparing 16s amplicon and metagenomics data using human gut samples [1]. A similar approach will be taken for pig gut metagenomics data using the Common Workflow Language for its development.

References:
[1] Usyk, Mykhaylo, et al. "Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies." Cell Reports Methods 3.1 (2023).
Used skills Common Workflow Language.
Requirements Basic bioinformatics knowledge.