121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown

In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of organisms from their renowned collection, tackling the challenges of assembling complex genomes from bacteria, viruses, fungi, and more. Discover how Nikhita and her team navigate through genomic roadblocks, leverage cutting-edge sequencing technologies, and work to ensure accurate data provenance. Whether it's large viral genomes or evolving taxonomy, this episode offers a deep dive into the fascinating world of microbial bioinformatics and genomic curation.

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.

In this episode of the Micro Binfie Podcast, host Andrew Page speaks with Dr. Brooke Talbot, a recent PhD graduate from Emory University, about her research on Staphylococcus aureus, with a focus on MRSA and antibiotic resistance. Brooke shares insights into her molecular epidemiology work, discussing the complexities of tracking resistant bacterial strains in clinical settings and the significance of genomic epidemiology in public health. From honeybees to foodborne outbreaks, Brooke’s diverse research background offers listeners a fascinating journey through science, microbiology, and epidemiology.

In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin shares her journey from researching hereditary cancer predisposition to her current role in public health bioinformatics, which she entered through a prestigious CDC and APHL fellowship. The conversation delves into her work with bacterial pathogens, particularly in tracking antimicrobial resistance in organisms like Klebsiella. Erin discusses the tools she uses for genome typing, such as MASH, FastANI, and SKA, and her innovative research on the accuracy of long-read sequencing technologies like Nanopore for detecting antimicrobial resistance genes. She also provides a preview of her upcoming poster for ASM, where she examines how Nanopore reads can be used effectively in public health microbiology. This episode offers a fascinating look at how bioinformatics and genomics are advancing the fight against infectious diseases.

In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits down with David Mahoney, a PhD student from Dalhousie University in Halifax, Nova Scotia. David shares his research on characterizing antimicrobial resistance (AMR) genes and their transfer within metagenomes, focusing on metagenomic assembly graphs. They delve into David’s background in food safety microbiology and his interest in the public health implications of genomics. He explains his exciting work on analyzing how AMR genes transfer across different environments, such as food production plants and clinical settings, using both new and existing data from Canada’s Genomics Research and Development Initiative. David also highlights his use of innovative methods like assembly graphs and graph-based approaches to uncover AMR gene flow and lateral gene transfers, including the potential of machine learning techniques such as graph convolutional neural networks.

In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by labs worldwide, and the explosion of tools post-COVID. Torsten shares insights into his work at Melbourne’s Microbiological Diagnostic Unit (MDU), the development of platforms like OzTracker for bacterial genomics, and how his lab plays a national and international role in data sharing. The conversation dives into the future of the widely-used variant calling tool Snippy, as Torsten reveals exciting updates funded by the Chan Zuckerberg Initiative, including nanopore read support and the ability to process pre-assembled genomes. They also explore the importance of maintaining open-source bioinformatics tools to prevent them from becoming obsolete. Tune in for an in-depth discussion on the state of genomics, software development, and the challenges and rewards of open-source collaboration.

In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. Tim shares insights from his work at Utrecht University in the Netherlands, where he focuses on genomic surveillance and machine learning models to predict disease risk and severity. They discuss the challenges of integrating genomic variation into predictive models, the importance of high-quality metadata, and the complexities of working with pathogens like Shiga toxin-producing E. coli. Tim also talks about his role at the WHO Pandemic and Epidemic Intelligence Hub and how global collaboration can drive innovation in public health genomics. Tune in to hear about cutting-edge research, the importance of interdisciplinary teamwork, and how genomic data can be harnessed for future pandemic preparedness.

Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insights into how this end-to-end tool is transforming bacterial genomic surveillance. They dive into the origins of Bactopia, its applications in public health, and Robert's experience leading genomic projects in a rural setting. Discover how Bactopia streamlines pathogen detection, improves documentation, and integrates with other tools to deliver fast and accurate results. Listen in as they discuss new innovations in bioinformatics, including visualizations and human-read filtering, and explore future projects like CamelHUMP, designed to simplify sequence-based typing. Recorded live at the Microbial Bioinformatics Hackathon in Bethesda, Maryland, this episode brings you the latest in pathogen genomics and the challenges and rewards of working on the frontier of public health.

Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190 Walters et al, "Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 reveal relatedness to previously circulating strains" https://journals.asm.org/doi/abs/10.1128/jcm.00142-23

Nabil and Lee have a quick chat about minimum spanning trees (MST). Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-152