Developing an assembly and annotation pipeline for gut bacterial genomes
Ashley Wolf, Professor
Public Health
Closed. This professor is continuing with Fall 2024 apprentices on this project; no new apprentices needed for Spring 2025.
Bacteroidetes is one of the main bacterial groups of the human gut microbiome. Although several reference strains related to species such Bacteroides thetaiotaomicron, Bacteroides fragilis and Phocaicola vulgatus have been investigated and even used as model organisms to understand the gut microbiome, strain level diversity is extensive and remains to be identified and characterized. The Wolf lab has a large collection of native Bacteroidetes strains, which are important degraders of fiber in the human intestine. We have recently whole genome sequenced these strains and are beginning to analyze this data. This project seeks to develop a bioinformatic pipeline to assemble, annotate and characterize these genomes, which will allow further interrogation of their potential metabolic capabilities.
Role: Pipeline development, genome annotation, data analysis
Qualifications: Student should have data science/computer science coursework or previous programming experience (required) and some biology (preferred)
Day-to-day supervisor for this project: Vienvilay Phandanouvong-Lozano, Post-Doc
Hours: 6-8 hrs
Related website: awolflab.com
Biological & Health Sciences