| 0830 – 0900
0900 – 1600 |
Registration for workshop
Workshop |
| OPTIONAL – Installation of required software Dr Michael Roach & Professor Rob Edwards |
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| Challenges associated with viral metagenomics Scott Handley, PhD |
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| BREAK | |
| Viral enrichment and DNA extraction methods Professor Rob Edwards |
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| Running Hecatomb demonstration Dr Michael Roach & Scott Handley, PhD |
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| LUNCH (not provided) | |
| Hands-on part 1: Loading files and filtering alignments Dr Michael Roach |
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| Hands-on part 2: Visualisation and statistical interrogation Dr Michael Roach & Professor Rob Edwards |
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| BREAK | |
| OPTIONAL – Hands-on extra help and troubleshooting Dr Michael Roach & Professor Rob Edwards |
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| Workshop ends | |
Abstract:
One virus has been at the forefront of everyone’s mind recently, however, the impact from the pandemic is a drop in the ocean compared to the impact that viruses (including bacteriophages) have on our daily lives. Viruses are a core component of every microbiome, and they influence every environment including human health and disease. While some are associated with disease states, most viruses are harmless or even beneficial. For instance, there is a renewed interest in the use of phages for combating the rise of antimicrobial resistance.
Viral metagenomics is fraught with challenges. Viruses are both highly diverse and poorly represented in reference databases. Viruses share large portions of sequence homology with other domains of life. Viral metagenomics studies are hence typically populated with false-positive hits while novel viruses fly under the radar. We’ve developed Hecatomb to address these issues and make accurate viral metagenomics accessible to anyone.
This workshop will cover an overview of the challenges associated with:
- Viral metagenomics; methods and approaches for viral enrichment and DNA extraction in the lab
- A detailed overview of installing and running the Hecatomb pipeline for different platforms and usage cases
- An extensive hands-on component for visualizing and statistically interrogating your data.
By the end of this workshop, you will have everything you need to perform your own viral metagenomics analysis.
Professor Robert Edwards
After receiving his Ph. D. from the University of Sussex, in England studying nitrogen regulation in bacteria, Dr. Edwards moved to the United States to continue his studies. He worked as a Post-Doctoral Researcher at the University of Pennsylvania, Philadelphia, understanding how a leading cause of traveller’s diarrhea (E. coli)causes disease. Dr. Edwards then moved to the University of Illinois, Urbana Champaign to study another food-borne pathogen, Salmonella. These studies merged the nascent area of genomics with traditional microbial genetics to investigate how a particular type of Salmonella became the leading cause of food-borne illness in the United States.
From 2000 to 2004, Dr. Edwards was an Assistant Professor at the University of Tennessee Health Sciences Center in Memphis, TN. Here, Dr. Edwards continued his studies on pathogenic bacteria, notably Salmonella and the bioterrorism weapon Francisella. Dr. Edwards received FBI clearance to work on these bacteria and was invited to the NIH to comment on the use of Select Agents at basic research laboratories.
In 2004, Dr. Edwards moved to the non-profit Fellowship for Interpretation of Genomes to work at the interface of biologists and computer scientists and worked with their team at Argonne National Laboratory. He remains an active software developer for Argonne and the Fellowship, developing open-source software including PERL and Python software for biological analysis and parallel computing that are used by scientists worldwide. Using breakout DNA sequencing technologies, Dr. Edwards’ studies have continually pushed the forefront of both sequencing technology and bioinformatics. His work has been published in leading journals including multiple papers in both Nature and Science.
Dr. Edwards returned to academia in 2007, taking a research and teaching position in the Departments of Computer Science and Biology at San Diego State University where he rose through the ranks to become a Full Professor. He continued to work at the interface of biology and computing. The National Institutes of Health, the National Science Foundation, the Department of Education, the Department of Defense, the USGS, and private donors funded Dr. Edwards’ research at SDSU, and his work led to breakthroughs in our understanding of how viruses interact with their hosts, and how viruses from around the world carry important genetic information. Dr. Edwards has continued to push current sequencing and bioinformatics technologies, in 2013 took a next-generation sequencing machine to the remote Southern Line Islands to explore metagenomics of coral reefs in real-time. In 2014 Dr. Edwards’ team identified a virus that is present in the intestines of approximately half the people in the world, and in 2019 Dr. Edwards demonstrated the global spread of the virus in a paper that includes collaborators from every continent who collected and sequenced samples. In 2017, Dr. Edwards was elected to the American Academy of Microbiology in recognition of his contributions to the field of microbiology. In 2020, Dr. Edwards took the position of Matthew Flinders Fellow in Bioinformatics at Flinders University, in Adelaide, South Australia, Australia to start the Flinders Accelerator for Microbiome Exploration, to enhance microbiome and metagenome studies in South Australia.
Committed to teaching, Dr. Edwards received the graduate student award for the outstanding educator at the University of Tennessee, the teacher-scholar award and outstanding faculty award four times at San Diego State University. He was Graduate Advisor to the Biological and Medical Informatics Program at SDSU. Rob travels extensively to share his passion for bioinformatics and has taught bioinformatics classes around the US, and in Australia, China, Chile, Europe, Mexico, and North and South America. Dr. Edwards holds a visiting professor position at the Federal University of Rio de Janeiro.
In addition to science and teaching Dr. Edwards is also an advanced scientific SCUBA diver having led teams to study Coral Reefs all over the world. In his spare time, he is an avid international yachtsman, navigating in long-distance offshore races, including navigating the 2019 TransPac race from Los Angeles to Honolulu finishing 4th out of 89 boats.
A/Prof Scott Handley
For the past 15 years, Scott has been involved in projects devoted to the advanced understanding of how microbial ecology and invasive pathogens operate and impact human health.
His view of how microbial ecology can contribute to disease comes in two forms:
The first is more traditional in which the introduction of an invasive organism (pathogen) negatively impacts either the host or the other members of the microbial community.
The second form is when an imbalance in the community itself leads to disease (dysbiosis).
His overall research goal is to better classify and test how alterations in community membership and function contribute to disease. To do this, he utilized high-throughput sequencing technologies, computational tools and community ecology analysis. Most of this research occurs in the mammalian gastrointestinal tract, however, lessons learned should be broadly applicable to studies at other sites.
Dr Michael Roach
Dr Roach is the the Bioinformatician at the new Flinders Accelerator for Microbiome Exploration (FAME). At FAME, they apply metagenomics to obtain a better understanding of the microbiomes associated with various environemental and human health issues. His research interests include all things bioinformatics, data viz and graphic design, software dev, and more recently webapp dev.
He previously worked at the Australian Wine Research Institute (AWRI) where he assembled the Chardonnay genome and developed the new gold standard for grapevine clonal marker discovery. He wrote the pipeline Purge Haplotigs for heterozygous diploid assembly clean-up, and contributed to many other various yeast genomics projects.
Prior to the Post-doc at the AWRI, his Honours and PhD projects were in drug discovery, not genomics, and involved identifying and testing candidate structural inhibitors of malarial enzymes which required a lot of protein homology modelling and in silico screening.