A/Professor Torsten Seemann
Victorian Life Sciences Computation Initiative and Microbiological Diagnostics
Unit Public Health Laboratory, The University of Melbourne
How do we generate the genome sequence of our favourite organism? In this talk I will introduce the problem of de novo genome assembly; describe the strategies and caveats of the way the problem is tackled; and outline ways to assess the results. The related problems of transcriptome and metagenome assembly, and how the latest technologies are transforming de novo assembly, will also be touched upon.
A/Prof. Torsten Seemann is lead bioinformatician at the Victorian Life Sciences Computation Initiative and the Microbiological Diagnostics Unit Public Health Laboratory, both at the University of Melbourne. His work uses bioinformatics and genomics to better understand the spread and evolution of bacterial pathogens and antimicrobial resistance. He is best known for his software tools which are used internationally, and he is a strong supporter of open science.
This talk will discuss methods for comparing large numbers of bacterial isolates at the small scale (such as SNVs) and the large scale (pan-genome content). The methods, important caveats and visualisation of bacterial population SNV and pan-genome determination will be covered. These techniques are now becoming applicable to metagenomic data sets now because increasingly long sequence read length makes it possible to extract individuals from a population.