Microbiome strain-level analysis using long read sequencing

Microbiome strain-level analysis using long read sequencing

Project details

Technologies and analysis tools are being developed to enable understanding of communities of microbes - microbiomes. A key aspect is knowing, at the finest genomic level (strain level), what microbes are present, their relative abundance, and details of specific genes present.  This project concerns using sequence data from the latest long read technologies to identify important genetic features of strains in a microbiome. 

Project
  1. Assess the feasibility of building more accurate genomic sequences for those strains present in a microbiome sample. 
  2. Investigate methods to genetically characterise bacterial strains in a microbiome sample using only long reads, long combined with short reads, and possible improvement to recently published methods.

The Speed Lab has expertise in long read sequencing analysis and its application to microbiomics..

About our research group

The Speed Laboratory addresses a broad set of challenges in transforming raw quantitative data from biological and biomedical studies into valid and understandable form.  This includes development of improved statistical techniques for combining data across collection conditions, finding better ways to extract and interpret single cell expression from various technologies, and extending machine learning techniques to extract base modification data from nanopore sequencer signals.

 

Email supervisors

 

Researchers:

Profile photo
Dr
Chris
Woodruff
Bioinformatics division

Project Type: