Micro Binfie podcast

#Science #Micro Binfie #Microbial Bioinformatics

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Cooking show host Sunny Anderson was only nineteen when she was diagnosed with ulcerative colitis, a form of Inflammatory Bowel Disease. But as Sunny puts it, "it sure as heck didn't pick the weak one!" Alongside board certified gastroenterologist Dr. Aja McCutchen, our guests discuss how this disease specifically affects women and Sunny shares her experience of living loud and proud with UC. If you've been recently diagnosed, this candid and informative discussion is an excellent starting place as you begin to navigate a life with UC. Resources : ThisIsLivingWithUC.com Note : This podcast is provided for educational purposes only and is not meant to replace discussions with a healthcare provider. Please speak with your healthcare provider regarding any health questions. The opinions expressed in this podcast are the opinions of the individuals recorded and are not necessarily opinions endorsed by Pfizer. Guests in this podcast were compensated for their time. This podcast is only intended for residents of the United States. _______________ Women's Health is your destination for compelling, stand-out series that touch on all aspects of women's health. While each series may focus on a different topic, they're united in their commitment to candid conversations that destigmatize women's health issues and highlight real life people. Learn more about each series featured below: menopause: unmuted is honest, hopeful, life-affirming, and features real women talking candidly about their menopause, and its impact on relationships, friends, family, and work. Each episode shares deeply personal accounts of the different emotional and physical symptoms experienced. Our host, leading women’s health expert Dr. Mary Jane Minkin, provides an expert perspective, busting myths and offering evidence-based information. These podcasts are not designed to provide medical advice or promote or recommend any treatment option. This podcast feed is powered by Pfizer. Hosted by Simplecast, an AdsWizz company. See pcm.adswizz.com for information about our collection and use of personal data for advertising.…

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Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics. The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics. Intro music : Werq - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Question and comments? microbinfie@gmail.com

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Micro binfie podcast

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147 episoder

#Science #Micro Binfie #Microbial Bioinformatics

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Micro binfie podcast

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144 - micro binfie Pathoplexus part 1 22:47

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Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team…

Micro binfie podcast

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143 - where we catch up on our professional lives 13:05

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143 - where we catch up on our professional lives by Microbial Bioinformatics

Micro binfie podcast

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142 - Microbinfie - genomeqc 26:42

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The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.

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140 Exploring Clinical Metagenomics 22:54

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In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying pathogens in clinical samples when traditional diagnostic methods fail. They discuss the types of samples analyzed, the impact of low DNA concentrations, and the complexities of sequencing data interpretation. The conversation highlights the importance of interdisciplinary collaboration between bioinformaticians and clinicians in managing difficult infections. Despite the hurdles, clinical metagenomics is presented as a complementary tool aiding in diagnosis, emphasizing the need for genomic literacy among healthcare professionals.…

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139 Lassa virus genomics 15:29

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On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challenges in the field, including the rapid detection of AMR using nanopore sequencing, COVID-19 projects, hepatitis A outbreak investigations, and Lassa virus surveillance in Liberia. The guests share insights into their professional journeys, their experiences working across different continents, and the future of microbial bioinformatics research.…

Micro binfie podcast

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138 Decoding Tetracycline Resistance in MRSA 11:24

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In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory University. Megan delves into her research on Staphylococcus aureus (MRSA), highlighting its fascinating dual nature as both a harmless and potentially serious pathogen. Megan discusses the complexities of tetracycline resistance, particularly focusing on plasmid-mediated mechanisms involving the pt181 plasmid. She explains how this plasmid’s efflux pump, encoded by the gene tetK, contributes to variable resistance levels and the factors influencing MIC (Minimum Inhibitory Concentration) variability. Listeners will learn about the intricacies of plasmid copy numbers, their global spread across clonal complexes, and the occurrence of horizontal and vertical gene transfer. Throughout the episode, Megan shares insights on working with short-read sequencing data and the strategies she employs to detect plasmid presence using tools like BLAST. She also touches on the challenges and fascinating discoveries of tracking historical sample data and integrating findings from older research papers, showcasing her appreciation for the poetic style of scientific writing from the 1940s. For those interested in antimicrobial resistance, evolutionary microbiology, and the subtleties of bacterial genome analysis, this episode offers a compelling blend of technical details and engaging storytelling. Tune in to hear more about Megan’s upcoming publications, her experiences navigating complex genomic data, and her thoughts on antimicrobial stewardship and historical perspectives on drug resistance.…

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137 Contagion part 2 32:26

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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.…

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135 Assembling ATCC bacterial strains 13:35

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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.…

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141 hackathon panel 15:20

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Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon

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90 Public health bioinformatics on the cloud with WDL + Terra.bio 44:19

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90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics

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89 What do we do with WDL? 26:08

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Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a shot at Lyve-SET and you'll never guess what happens next. In the MicroBinfie podcast, we discuss the workflow description language (WDL) commonly used to describe bioinformatics pipelines in a portable and cross-environmental way. The starting point is the presumption that tools are already containerized, and WDL helps to bind them together. The guests highlighted that this standardizes bioinformatics in the field, making it more reproducible and scalable. It also helps remove the need for excessive CIS admin work, enabling researchers to spend more time on scientific questions. Despite having many workflow languages available, WDL is unique in its formal specification and its orthogonality to the common implementations that are used in executing those things. In the second part of the podcast discussion, guests Joel and Danny talked about workflow languages and public health bioinformatics. They highlighted the challenge of version control to quality management and its effects on the field of bioinformatics. They spoke about the origins of the community, StaphB, which comprises state-level public health bioinformaticians. The community discusses various challenges and contributes to creating links between academia and state public health departments. WDL is a workflow language used for bioinformatics work that the hosts use. Danny shared his story of how they came to use Whittle and how they realized it was the perfect language for portability of pipelines. On the other hand, Joel talked about how they chose WDL for its applicability to public health and the support it received from its creators, particularly the Broad Institute. They both agreed that the choice of workflow language was driven by the environment they could work in and which language was best suited to their needs. In conclusion, the discussion focused on the vital role of workflow languages such as WDL in bridging the gap between bioinformatics and public health. The choice of workflow language was critical and would depend heavily on the environment in which the language was used. Finally, they expressed their support for WDL and how it had helped them streamline their bioinformatics workflows.…

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88 Sepia directors cut 53:01

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This is an extended directors cut of our chat with Dr Henk den Bakker about Sepia. Its a summer holiday bonus. Some URLs Get Sepia here: https://github.com/hcdenbakker/sepia Some information on the food safety informatics group at UGA: https://www.denglab.site/ Rust: https://www.rust-lang.org/ Kalamari: https://github.com/lskatz/kalamari CAMI: https://www.nature.com/articles/nmeth.4458…

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87 Nextstrain, SARSCOV2 and dealing with a data deluge 27:56

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87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics

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86 What's next for nextstrain? 22:55

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86 What's next for nextstrain? by Microbial Bioinformatics

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85 Breaking the dogma with bioinformatics 27:15

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We are joined again by Prof Mark Pallen who takes us through his early experiences in high-throughput microbial genomics. Mark was pleased that he persuaded Nick Loman to join him in Birmingham. Mark tells us how they worked with George Weinstock to perform the first genome sequence analyses of Gram-negatives for genomic epidemiology—in this case of multi-drug resistant Acinetobacter baumannii. After winning an Ion Torrent sequencer in a competition, Mark and Nick then contributed some pioneering genomic analyses of the German STEC outbreak. One of their studies involved crowd sourced approaches, primed by Twitter and was published in the New England Journal of Medicine; the other provided a performance comparison of newly launched bench top sequencing platforms. Mark, Lee and Nabil discuss how this outbreak overturned dogmas concerning the archetypal status of pathotypes of E. coli. The conversation then moves on to the need for evidence trails and challenging assumptions, whether annotating proteins or quoting Darwin (see https://colinpurrington.com/2012/02/darwin-on-the-floor-lhao/). Nabil recalls the excitement of realtime analysis of an epidemic and acknowledges the legacy of Mark and Nick's work in 2011 to current approaches to the Covid pandemic. Mark describes his exciting experiences exploiting metagenomics in clinical and ancient DNA contexts, including analysis of disease-associated stool samples and of 200-year TB genomes in Hungarian mummies. Yet again this led to overturning of assumptions--in this case that people only get infected with a single strain of M. tuberculosis. It turns out that multiple infections were the norm 200 years ago. Shortly afterwards, Pallen helped assemble a team that analysed undersea sediments shedding light on the Neolithic transition in England and culminating in a Science paper. Mark then takes us through his recent metagenomics analyses of critically ill patients and of the chicken gut, emphasising the excitement of finding hundreds of new species in such a commonplace setting. Mark finishes off by sharing his excitement that there is still so much of the microbial world left for us to discover using sequencing and bioinformatics analyses. We are just 2% of the way there!…

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84 Bioinformatics in the noughties with Mark Pallen 22:14

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Mark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time from model organisms and fearsome pathogens. He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Pallen describes the addictive exhilaration of using PSI-BLAST to find new sortases and sortase substrates across a range of new genomes—for him this was the bioinformatics equivalent of crack cocaine. He quotes the philosopher Alfred North Whitehead in saying that the goal of every scientist is to seek simplicity but distrust it. What Mark found was that in most organisms sortases were behaving quite differently from the rather simple scenario seen in Staphylococcus aureus. He made similar observations on the WXG100 proteins and type VII secretion, which he found in many new contexts quite different from the original context of ESAT-6 as an antigen in Mycobacterium tuberculosis. Mark makes clear that we still don't really fully understand the role of ESAT-6 twenty years on. The focus of Pallen's work then shifted to E. coli, where he described vestigial gene clusters for non-functional type III secretion systems in this model organism. He came to realize that E. coli K-12 was not handed to microbiologist by God as a model organism but was just another strain of E. coli and nothing special. Many of the earliest genomes to be sequenced came from worn-out lab strains. To counter this problem, Gordon Dougan at the Wellcome Trust Sanger Institute moved the focus to genome-sequencing freshly isolated minimally passaged isolates. With Brendan Wren, Pallen wrote a review article for nature, emphasizing the importance of adopting an eco-evo perspective when trying to interpret bacterial genomes. Around that time, Scott Beatson joined Pallen's group. Mark managed to persuade Scott to work on type III secretion in E. coli rather than Pseudomonas aeruginosa. The result was the discovery of dozens of new type III secretion effectors, tying together bioinformatics and lab work to culminate in a PNAS paper. References - https://microbinfie.github.io/2022/06/09/bioinformatics-in-the-noughties.html…

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83 A short journey into mobile genetic elements 17:39

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We discuss mobile genetic elements in bacteria and find, its really hard. Its just a short chat as Lee lost power, but we will be back with a part 2 sometime soon.

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82 Bioinformatics moments before the millennium 39:57

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In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician. His bioinformatics journey began in 1977, the year Fred Sanger invented DNA sequencing-as-we know-it, when Mark was tasked with assembling some amino acid sequences under exam conditions. Mark explains how little was know about sequences at the time. Luckily he managed to gain a grasp of molecular biology and joined a group in the late 1908s at Barts Hospital in London, where he met Brendan Wren. Mark's first eureka moment followed shortly afterwards, when he analysed sequences encoding the key enzyme urease from Helicobacter pylori. He also got very excited when he analysed genes from a clostridial butanol fermentation pathway, which he explains, played a central role in the formation of the state of Israel. His next big break came when he got the chance to do a PhD under Gordon Dougan. During this time, Mark not only improved his lab and bioinformatics skills, but captained a winning team in University Challenge and introduced the medical profession to the Internet. He recalls with excitement the moment when he first heard the news that a bacterial genome had been sequenced. Shortly afterwards he recruited an 18-year old gap year student, Nick Loman, to come and work with him analysing the very first Campylobacter jejuni genome. We close this episode just as the new millennium begins, with much more excitement to follow in the next episode. Relevant links: Butanol - https://academic.oup.com/femsle/article/124/1/61/486499 Tree-like thinking for genes, languages and gospel manuscripts - https://www.youtube.com/watch?v=8Ykj5wQs7vU Further references - https://microbinfie.github.io/2022/05/12/bioinformatics-moments-before-the-millennium.html…

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81 The people behind the benchmark datasets for SARS-CoV-2 9:27

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We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2. See our previous episode for part 1 of the conversation. * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/…

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80 Benchmark datasets for SARS-CoV-2 43:05

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We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2 * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/…

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79 StaPH-B: Stable containers for public health bioinformatics 28:17

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Dr Erin Young from the Utah Department of Health and Dr Kelsey Florek from the Wisconsin State Laboratory of Hygiene join us to talk about StaPH-B containers for public health bioinformatics. Its basically how to make biology easier for everyone! Github: https://github.com/StaPH-B

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78 StaPH-B: state public health bioinformatics 25:33

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Dr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into the popular SARS-CoV-2 pipeline cecret. Website: staphb.org/ Cecret Pipeline: github.com/CDCgov/SC2CLIA Kelsey explains that StaPH-B was created to facilitate collaborations between bioinformaticians in state public health laboratories, especially those just getting started with sequencing and understanding the data generated. The organization provides a conduit of communication and expertise among different laboratories, feeding into projects funded by the NIH, CDC, and other grant agencies. Erin highlights StaPH-B's diverse membership with different levels of expertise, which provides excellent learning opportunities. The organization uses a Slack workspace, with almost 400 members and over 50 channels dedicated to different activities related to bioinformatics, providing a valuable resource for bioinformaticians to seek out answers to questions and ideas. The hosts ask Kelsey about who can join StaPH-B, and Kelsey clarifies that while it was initially founded for state public health bioinformaticians, it's open to everyone, and the content is focused on state public health activities. They discuss some of the achievements of StaPH-B, with Kelsey hailing the Slack workspace, collaborations on GitHub, Docker, and collaborative workflows as hugely successful. Additionally, Erin thinks that StaPH-B's training activities, including the Staph-B Toolkit, training sessions, and videos, ensure that knowledge and expertise are shared. The conversation moves towards the Cecret pipeline, one of Erin's bioinformatics pipelines for SARS-CoV-2. She explains that the pipeline was developed during the pandemic, with the idea of using the Arctic group's protocol for sequencing SARS-CoV-2 on the Nanopore sequencing platform. However, Erin needed a bioinformatic pipeline that was Illumina-based, as it would have been easier to sequence SARS-CoV-2 on the MiSeq, rather than the Nanopore sequencing platform. Cecret pipeline was developed using BWA as the default aligner and is for viral-based sequencing with a known, reliable reference. Erin points to the SEQret pipeline tutorials and the monthly videos produced by StaPH-B that outline various state laboratory projects as tips for people entering the field. Lastly, Kelsey emphasizes the importance of finding a use case to start building a centralized source of expertise in bioinformatics and making knowledge accessible by having a common resource that's easy to access. In a previous episode, the guest speakers discussed the evolution of COVID genome analysis workflows and how they have changed over time due to the increasing amount of data being analyzed. They mentioned the use of different workflows such as Secret, NF Core, Monro, and Next Flow Optic Pipeline, each with their own unique features and popularity. Erin, the creator of Secret, talked about how paranoid she was when sharing her workflow publicly and how she would track every fork of her repository to ensure that the changes made to her code were scientifically sound. The workflow has undergone gradual changes and fewer bugs since its creation, with no dramatic turning point. Its name, “Secret,” was inspired by a hiking landmark in Northern Utah that Erin found meaningful. The speakers emphasized the importance of managing and working with the increasing amounts of COVID data being analyzed, as well as connecting it to public health. In conclusion, StaPH-B and workflows such as Secret are playing a significant role in the field of bioinformatics and COVID genome analysis. Collaborations and resources like StaPH-B are essential in sharing knowledge and expertise among different laboratories, allowing for the successful completion of projects funded by the NIH, CDC, and other grant agencies.…

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77 Genomics for a new era 38:16

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Today we’re talking about some exciting new developments in the area of comparative genomics. We are joined by Dr. Zamin Iqbal who is a Research Group Leader at the European Bioinformatics Institute and Dr. Grace Blackwell who is jointly at the European Bioinformatics Institute, in Zam’s group and Nick Thomson’s team at Wellcome Sanger Institute…

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76 What are the major challenges for getting AMR genomics into the clinic? 41:12

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What are the major challenges for getting AMR genomics into the clinic? This was the question poised to a panel of experts at the 7th Microbial Bioinformatics hackathon run in conjunction with JPIAMR, PHA4GE and CLIMB. The panel were: Mark Pallen from the Quadram Institute Bioscience, UK, Finlay Maguire from Dalhousie University, Canada, Anthony Underwood from the Centre for genomic pathogen surveillance, UK and Clement Tsui from the Weill Cornell Medicine, Qatar. Andrew Page was the Chair, supported by Lee Katz.…

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74 SEPIA With Henk - Soup Or Salad Yes! 37:36

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74 SEPIA With Henk - Soup Or Salad Yes! by Microbial Bioinformatics

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73 Bactopia and using workflow managers in bioinformatics part 2 28:35

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We are again joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20…

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72 Bactopia and using workflow managers in bioinformatics part 1 35:10

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We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20

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71 Bacterial taxonomy: Into the unknown, SeqCode, naming uncultured multitudes and renaming of phyla 40:59

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We finish our discussion on bacterial taxonomy, this time looking at new approaches of naming the multitudes of unnamed uncultured organisms and the controversial renaming of phyla. With guests Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf…

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70 Bacterial Taxonomy: the grand vista is ahead of us 28:40

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We continue our discussion on bacterial taxonomy, this time looking at how genomics has changed taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf…

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69 Background to bacterial taxonomy 26:29

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There has been a lot of discussion about bacterial taxonomy recently announced regarding phyla, and this revealed a lot of misconceptions around taxonomy in general. Today we discuss the background to bacterial taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/raw/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf…

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68 Bacterial Taxonomy: what is a species, what is a strain? part 2 40:54

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68 Bacterial Taxonomy: what is a species, what is a strain? part 2 by Microbial Bioinformatics

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67 Bacterial Taxonomy: what is a species, what is a strain? 25:25

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We’re navigating the twisted world of bacterial taxonomy. We have some excellent guides to help us! Our guests today are: Dr. Leighton Pritchard: Who is a Strathclyde Chancellor's Fellow at Strathclyde Institute of Pharmacy and Biomedical Sciences in the University of Strathclyde Dr. Conor Meehan: Dr. Conor Meehan is an assistant professor in molecular microbiology at the University of Bradford.…

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66 Scholarly Communications for Bioinformaticians 44:52

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Have you ever read a paper and wondered why the author buried their key result on page 39 of a 50 page paper? Bioinformaticians aren't great at communicating themselves or their science to the wider world, so we have a chat about it, specifically with bioinformaticians in mind. Topics include: Online presence/ scholarly communications for bioinformatics Google scholar/Scopus Marketing to a set of peers organisation websites managing publication record librarians citation metrics peer review twitter blogs personal webpage github for personal webpages sign up to github --help citation and name making your code public as you develop it. links in your signature self promote at end of slides just starting out Links: How to pronounce ORCID - https://info.orcid.org/how-should-orcid-be-pronounced/#:~:text=But%2C%20for%20those%20who%20want,pronounced%20%E2%80%9Coar%2Dkid%E2%80%9D. Phil Ashtons blog: https://bitsandbugs.org/ Publons: https://publons.com/about/home/…

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75 How to review a bioinformatics paper in 10 days or less 31:12

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We discuss how to effectively review bioinformatics papers, what to look out for and tips for researchers to when writing bioinformatics or microbial genomics papers to ease their way through review.

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65 Genomics of Mycobacterium tuberculosis 33:54

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We’re continuing our series where we examine a particular microbial species in some depth. We’re continuing our look at Mycobacterium tuberculosis, focusing more on bioinformatics, genomics and typing. Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan assistant professor in molecular microbiology at the University of Bradford.…

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64 Mycobacterium tuberculosis: the forgotten pandemic 36:24

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We’re continuing our series where we examine a particular microbial species in some depth. We’re talking about mycobacterium tuberculosis, the forgotten pandemic. Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan assistant professor in molecular microbiology at the University of Bradford.…

Micro binfie podcast

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63 A dive into Campylobacter genomics 33:57

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Our guest today is Dr Ozan Gundogdu for a deeper dive into the food borne pathogen Campylobacter and how genomics has informed the field over the past 20 years since the publication of the first reference genome in 1999. Ozan leads the foodborne enteric pathogen group at the London school of hygiene and tropical medicine. Where they study the physiology and pathogenesis of Campylobacter and other related enteric microorganisms like Listeria and Vibrio. His background is in Molecular Biology and Computer Science and he completed his PhD at LSHTM (London School of Hygiene & Tropical Medicine) in 2011. www.lshtm.ac.uk/aboutus/people/gundogdu.ozan…

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62 Campylobacter: the fussy little pathogen 21:42

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Our guest today is Dr Ozan Gundogdu and he gives us a crash course in food borne pathogen Campylobacter. If you've ever had a dodgy tummy after eating undercooked chicken, Campy is probably the cause. Ozan leads the foodborne enteric pathogen group at the London school of hygiene and tropical medicine. Where they study the physiology and pathogenesis of Campylobacter and other related enteric microorganisms like Listeria and Vibrio. His background is in Molecular Biology and Computer Science and he completed his PhD at LSHTM (London School of Hygiene & Tropical Medicine) in 2011. https://www.lshtm.ac.uk/aboutus/people/gundogdu.ozan…

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61 Non FUNGIble tokens: you too can own BRCA1 28:25

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We look at the crazy world of NFTs (non fungible tokens) and blockchain and explore in a light hearted way how they could be used in genomics and bioinformatics. We propose a way of replacing all the central genome databases and our own cryptocurrency (BioBucks or maybe GenomeCoin). Myriad genetics SCOTUS decision - https://www.supremecourt.gov/opinions/12pdf/12-398_1b7d.pdf Planet money episode on patenting a gene - https://www.npr.org/transcripts/937167323 Beeple - https://www.theverge.com/2021/3/11/22325054/beeple-christies-nft-sale-cost-everydays-69-million Make NFT - https://www.coindesk.com/how-to-create-buy-sell-nfts…

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Encore: 06 - What software not to write 43:45

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43:45

Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prokka, Snippy, Barrnap, Abricate, Shovill, and Nullarbor. Links: https://github.com/tseemann

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60 Whats in a name: Salmonella and E. Coli 28:56

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28:56

Today we’re talking about getting your head around our favourite enteric microbes. E. coli and Salmonella. Why do they have some of the names they have? Primer on ANI: https://www.pnas.org/content/102/7/2567.short Wikipedia on Salmonella serovars: https://en.wikipedia.org/wiki/Kauffman%E2%80%93White_classification Nabil's viral tweet: https://twitter.com/happy_khan/status/1387804862830809091?s=20…

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59 - Microbe Moment Micro Binfie 13:18

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Andrew, Nabil, and Lee answer the Microbigal's questions for the "Microbe Moment." You can find the Microbigals at https://www.microbigals.com

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58 - StaPH-B careers with Curtis Kapsak and Kevin Libuit 39:43

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We dive deeper into Curtis's and Kevin's career! Relevant links: https://www.skypeascientist.com/ https://www.aphl.org/fellowships/Pages/Bioinformatics.aspx https://www.jmu.edu/genomics/index.shtml jmu.edu/biology

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57 StaPH-B - Docker containers for Public Health bioinformatics Part 1 35:47

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The crew talks to Curtis Kapsak and Kevin Libuit about the StaPH-B containers. What a valuable resource! Some URLS: * StaPH-B docker-builds code repository: https://github.com/StaPH-B/docker-builds * StaPH-B DockerHub container repositories: https://hub.docker.com/u/staphb * Guide for contributing: https://staph-b.github.io/docker-builds/contribute/…

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56 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2 25:04

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Part 2 going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this method Kai Blin and Tue Jorgensen, both from the Technical University of Denmark. The preprint: www.medrxiv.org/content/10.1101/2….03.27.21252266v1 The protocol: www.protocols.io/view/sanger-sequ…-2-spik-bsbdnai6 The software: github.com/kblin/covid-spike-classification The web app: ssi.biolib.com/app/covid-spike-classification/run…

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55 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995 29:03

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Today we’re going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this method Kai Blin and Tue Jorgensen, both from the Technical University of Denmark. The preprint: https://www.medrxiv.org/content/10.1101/2021.03.27.21252266v1 The protocol: https://www.protocols.io/view/sanger-sequencing-of-a-part-of-the-sars-cov-2-spik-bsbdnai6 The software: https://github.com/kblin/covid-spike-classification The web app: https://ssi.biolib.com/app/covid-spike-classification/run…

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54 SARS-CoV-2 In Canada and addressing data sharing and privacy 26:02

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The Canadians have taken over the podcast - AGAIN ! Join guest host Dr. Emma Griffiths, as she talks with Dr. Finn McGuire and Dr. William Hsiao about the SARS-CoV-2 genomics epidemiology efforts in Canada. Cancogen website : https://www.genomecanada.ca/en/cancogen

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53 SARS-CoV-2 surveillance in Canada with CANCOGEN 33:06

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33:06

The Canadians have taken over the podcast ! Join guest host Dr. Emma Griffiths, as she talks with Dr. Finlay McGuire and Dr. William Hsiao about the SARS-CoV-2 genomics epidemiology efforts in Canada. Cancogen website : https://www.genomecanada.ca/en/cancogen

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52 SARS-CoV-2 sequencing in Denmark with Mads Albertsen 28:35

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28:35

Denmark is one of the leading countries in the world forSARS-CoV-2 genomic surveillance. Prof Mads Albertsen chats to us about SARS-CoV-2 sequencing in Denmark, how it got started, logistics, tweaked protocols and things hes learnt along the way. Edited by Niamh Page

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51 SARSCOV2 Round-up 3 and updates from Denmark 33:39

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We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Mads Albertsen and the latest developments in Denmark. Denmark covid stats: www.covid19genomics.dk/statistics Tools and resources mentioned: https://outbreak.info/ https://virological.org/t/outbreak-info-sars-cov-2-mutation-situation-reports/629 https://gitlab.com/johan.bernal.morales/sarscov2 Publications mentioned: A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols https://www.biorxiv.org/content/10.1101/2021.03.01.433428v1 Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report https://www.medrxiv.org/content/10.1101/2021.02.08.21251303v1 SARS-CoV-2 within-host diversity and transmission https://science.sciencemag.org/content/early/2021/03/09/science.abg0821 Info on masking SARSCOV2 sites: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 https://github.com/W-L/ProblematicSites_SARS-CoV2/blob/master/subset_vcf/problematic_sites_sarsCov2.mask.vcf…

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50 Atypical invasive non-typhoidal Salmonella in The Gambia 40:46

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Invasive non-typhoidal Salmonella is a significant public health challenge in Africa. We talk to Abdoulie Kanteh and Grant Mackenzie about their work in The Gambia, and their use of genomics to understand the serovars in circulation. Manuscript: https://www.biorxiv.org/content/10.1101/2021.02.18.431831v2…

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49 SARS-CoV-2 Tools and resources update 32:52

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32:52

We are joined by Peter van Heusden to discuss all the latest developments in SARS-CoV-2 genomics, particularly around tools and resources. We also discuss the challenges of building and sharing data in large scale sequencing endeavours. Tools and resources: Nextalign github.com/nextstrain/nextclade/releases COG mutation explorer http://sars2.cvr.gla.ac.uk/cog-uk/ Grinch https://cov-lineages.org New US tool for variants: https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/global-variant-map.html Online lineage assignment: https://pangolin.cog-uk.io/ CoronaHiT paper published: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5…

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48 SARS-CoV-2 More Variants of Concern and updates from Africa 28:58

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28:58

We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Peter van Heusden, covering the growing list of Variants of Concern and the latest developments in Africa. Papers & resources mentioned: American birds (677) - https://www.medrxiv.org/content/10.1101/2021.02.12.21251658v2 https://github.com/cov-lineages/pango-designation PHE thresholds for different variants: https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data A.23.1 in Uganda - https://www.medrxiv.org/content/10.1101/2021.02.08.21251393v1 B.1.525 - https://github.com/cov-lineages/pango-designation/issues/4 Zambia sequences - https://www.cdc.gov/mmwr/volumes/70/wr/mm7008e2.htm?s_cid=mm7008e2_w…

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47 SARS-CoV-2 Rapid roundup and questions answered 32:53

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32:53

We present a rapid round up of SARS-CoV-2 questions and issues, hopefully with some answers, so that you can stay on top of the latest in SARS-CoV-2 genomics. Recorded 5 February 2021. Topics covered: Why missing 1 SNP can cause lineage assignment to break and how it works? How do we describe lineages with a chain of mutation events? Are we seeing convergent evolution? Co-infections of different lineages discovered? For nanopore basecalling do use HAC & should you get a GPU? Basic logistics difficult for sequencing in many parts of world. Can I look at recombination with ARTIC on Illumina? How do you annotate a SARS-CoV-2 sequence? http://cov-glue.cvr.gla.ac.uk/#/home FASTA > nextclade VCF > snpeff https://github.com/cov-ert/type_variants Spotting community spread from NextStrain? Scientists call for fully open sharing of coronavirus genome data: https://www.nature.com/articles/d41586-021-00305-7…

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46 SARS-CoV-2 genomics resources 23:51

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23:51

We discuss recent updates to the best SARS-CoV-2 resources, so that you can stay on top of the latest bioinformatics and genomics tools. Recorded 5 February 2021. CoVariants website: http://covariants.org/ Microreact: https://microreact.org/project/cogconsortium/ Lineage reports: https://cov-lineages.org/ CLIMB ARTIC workshop online resources: https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/ Multiplex PCR for B.1.1.7, B.1.351 and P.1: https://www.protocols.io/view/multiplexed-rt-qpcr-to-screen-for-sars-cov-2-b-1-1-brrhm536 CDC videos: https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html…

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45 Software deep dive: Enterobase 20:48

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20:48

We chat with Nabil about EnteroBase, and learn about the background to the project, the general benefits of the platforms and some of the strange quirks users might encounter. EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Papers: Mentioned PLOS genetics paper: Alikhan et al. (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 14 (4): e1007261 https://doi.org/10.1371/journal.pgen.1007261 Paper describing Enterobase and the genome fishing expeditions: Zhou et al. (2020) The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity. Genome Res. 30:138-152. https://doi.org/10.1101/gr.251678.119 rMLST is described in: Jolley et al. 2012 Microbiology 158:1005-15. https://doi.org/10.1099/mic.0.055459-0 Resources Enterobase: http://enterobase.warwick.ac.uk/ PubMLST https://pubmlst.org/ About EnteroBase schemes: https://enterobase.readthedocs.io/en/latest/enterobase-tutorials/deeper-lineages.html Software: Enterobase toolkit and background software: https://github.com/zheminzhou/EToKi Errata. Jay Hinton’s Salmonella is a ST313 (D23580), not ST131 (I always mix the numbers up -- Nabil)…

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44 How to sequence SARS-CoV-2 using the ARTIC protocol with Joshua Quick 22:07

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22:07

Joshua Quick from the University of Birmingham talks about "How to sequence SARS-CoV-2 using the ARTIC protocol". This was part of a joint ARTICnetwork & CLIMB-BIG-DATA workshop on COVID-19 data analysis and chaired by Nick Loman. Links: https://twitter.com/Scalene/status/1349402397249056779 https://primalscheme.com/ https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye https://github.com/artic-network/rampart…

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43 Why use genomics in an epidemic? with Sam Sheppard 18:39

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Sam Sheppard from the University of Bath presents at the ARTICnetwork & CLIMB-BIG-DATA workshop on COVID-19 data analysis, motivating why we should use genomics in an epidemic. He gives background on typing schemes, different ways of sequencing and challenges such as how you can analyse large mounts of genomic data. Resources: https://sheppardlab.com/ https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/…

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42 Overcoming barriers to SARS-CoV-2 data analysis 46:30

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46:30

ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on overcoming barriers to SARS-CoV-2 data analysis with Nick Loman and Will Rowe from the University of Birmingham, Áine O'Toole from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis. Topics covered: Collecting sample metadata intrapatient variability Building bridges with policy makers to start sequencing Data sharing Improving bioinformatics skills Pipeline and software validation Bioinformatics reproducibility and quality Papers: The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology https://www.preprints.org/manuscript/202008.0220/v1 MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance https://www.biorxiv.org/content/10.1101/2020.10.06.328328v1 Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health https://www.who.int/publications/i/item/9789240018440 Resources: https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/ https://github.com/SamStudio8/majora https://soundcloud.com/microbinfie/majora https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification https://pha4ge.org/ Software: https://github.com/cov-lineages/pangolin https://github.com/artic-network/civet https://github.com/COG-UK/grapevine https://github.com/cov-lineages/pangoLEARN…

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26 SARS-CoV-2 contextual data specification for open genomic epidemiology 37:46

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37:46

We talk to Dr Emma Griffiths (UBC), Dr Ruth Timme (FDA) and Dr Duncan MacCannell (CDC) about the PHA4GE SARS-CoV-2 contextual data specification for open genomic epidemiology. Paper: https://www.preprints.org/manuscript/202008.0220/v1 Specification: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification Protocols: https://www.protocols.io/workspaces/pha4ge The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.…

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25 Sustainable bioinformatics software 27:09

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27:09

How do you make bioinformatics software sustainable so that we can move our field from academic research into hospitals and doctors offices? We discuss the nuts and bolts of making sustainable bioinformatics software and changes you can make in your own practices: Documentation, Coding styles, Versioning, SOPs and capturing institutional knowledge, Software licencing, Automated testing, Measuring your impact, and going the commercial route.…

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24 Experimental projects lead to experimental software 19:50

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19:50

Experimental projects lead to experimental software. We discuss the issues around the sustainability of academic bioinformatics software. How it currently works, why software dies, quality issues, and what we can do to keep it going.

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23 CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes on Nanopore 28:48

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28:48

We chat with the authors of CoronaHiT which lets you sequence up to 94 SARS-CoV-2 samples on a single MinION flowcell. This reduces the cost of sequencing 3-fold, with a simpler, faster protocol. Justin O'Grady and David Baker join Andrew Page and Nabil-Fareed Alikhan to chat about how it all works, how it came into being and why its awesome. Preprint: https://doi.org/10.1101/2020.06.24.162156…

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22 Assembly after party 32:06

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32:06

When you get an assembly the fun doesnt stop there. You then have to fix it up and see how good it is. In this episode we discuss scaffolding, gapfilling, polishing, assembly metrics, quality control, genome structure, and visualisation tools. Tools and papers mentioned: https://github.com/quadram-institute-bioscience/socru https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004446…

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21 Setting up coronavirus sequencing for real-time public health surveillance 28:58

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28:58

We chat to Justin O'Grady and Andrew Page on how to get a SARS-CoV-2 sequencing effort off the ground in the middle of a pandemic and go on to sequence 1,500 genomes in 2 months. The Quadram institute is one of 16 sequencing centres in the UK which are part of the COVID-19 genome sequencing consortium. Things we touch off include COG, contamination issues, the people, and bioinformatics. Further information from: https://www.cogconsortium.uk/ If you want to access the sequencing data produced by Quadram, please checkout the ENA and GISAID.…

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20 Assembly read healing 17:07

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17:07

Preprocessing of sequence data in advance of de novo assembly is a critical step to improving the final quality of your assembly. We chat about read trimming, correction and filtering, collectively called 'Read Healing'. Software mentioned: https://github.com/sanger-pathogens/plasmidtron

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19 Microbinfies assemble 25:24

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25:24

Short read de novo assembly is discussed in this podcast. We cover the history of assembly and how short read assemblers have evolved into what we use today. The main focus is on bacterial assembly.

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18 Panel - Has Nanopore rendered onsite Illumina obsolete? 19:09

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A panel discussion held in MRC Gambia at The London School of Hygiene and Tropical Medicine, recorded in front of a live audience of scientists in January 2020, when SARS-CoV-2 was just beginning to be reported as an emerging infectious disease. The panel consisted of Andrew Page and David Baker from the Quadram Institute, Ozan Gundogdu from LSHTM (UK), Abdul Sesay from LSHTM (Gambia) and Nick Loman from the University of Birmingham and chaired by Suzie Hingley-Wilson from the University of Surrey. Questions, discussion and comments from: Mark Pallen - Quadram Institute Muna Anjum - APHA Arnoud van Vliet - University of Surrey Martin Antonio - LSHTM Archie Worwui - LSHTM Unfortunately we weren't able to capture the audio from Nick Loman who joined via Skype, but he did make really great contributions.…

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17 Bayesian magic in practice 32:06

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32:06

The second part of the dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.

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16 The theory behind Bayesian Magic 47:40

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47:40

The dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.

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15 Bioinformatics war stories 10:39

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10:39

We share short war stories about bioinformatics from the trenches of research. We share tales about a mystery massive Listeria outbreak, bubbles on flowcells, GAII woes, contaminated databases, the mass murderer, water pouring into a sequencing centre, changing protocols without validation, Excel issues and the ultimate complexity in science - Humans.…

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14 La resistance lives on: The AMR deep dive 27:16

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27:16

Kate Baker talks AMR

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13 Questions not to ask 29:34

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Someone asks a simple question like "What programming language should I learn?", without realising just how difficult it is to answer. We discuss different programming languages and their use in Bioinformatics.

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12 Phylogenetics with the arborists part 2 32:01

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32:01

12 Phylogenetics with the arborists part 2 by Microbial Bioinformatics

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41 SARS-CoV-2 Phylogenomics questions answered 25:17

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25:17

ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on SARS-CoV-2 phylogenomics with Nick Loman from the University of Birmingham, Verity Hill from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis. The topics covered are: More about Polecat Whats the difference between COG-UK Phylotypes and Pangolin lineages? What is the difference between Civet and Llama Can you use BLAST to find similar SARS-CoV-2 genomes? How do you find similar sequences in the public repositories to give your samples context? How do you manually curate the dataset for PangoLEARN? How does Civet choose what constitutes a subtree? Can Civet be adapted to other viruses? Are the vaccine sequences available? Databases that report variation Quality of variant calls? Groups: https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/ https://www.climb.ac.uk/ https://artic.network/ https://cogconsortium.uk/ Software: https://github.com/COG-UK/polecat https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/llama https://github.com/artic-network/civet https://github.com/cov-lineages/pangoLEARN http://tree.bio.ed.ac.uk/software/figtree/ Analysis websites: https://cov-lineages.org/ https://clades.nextstrain.org/ https://pangolin.cog-uk.io/ http://cov-glue.cvr.gla.ac.uk/…

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40 A crash course in SARS-CoV-2 bioinformatics 57:26

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57:26

Over the last year we've learnt a lot about SARS-CoV-2 genomics. Lee extracts all the insider knowledge from our brains and we give him the honest truth to his probing questions. We cover: Pipelines for SARS-CoV-2 Archives & metadata Read filtering Assembly vs consensus Amplicon data analysis Controls If things look too good Coverage .... Some URLs: https://github.com/connor-lab/ncov2019-artic-nf https://github.com/jts/ncov-tools https://github.com/lskatz/SARS-CoV-2-trueTree…

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39 Explaining the naming of SARS-CoV-2 new variants 20:24

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20:24

Andrew talks to Niamh Tumelty from the University of Cambridge about SARS-CoV-2 'new variants' and tries to clear up some of the confusion around all the names flying around. Hopefully this helps to give some insights into the various names you hear, but probably by the time you listen the whole thing will have changed again since this field moves so rapidly. Andrew apologises in advance for all the errors that will be found in this podcast! If you want to read a bit more theres an interesting news item on Nature: https://www.nature.com/articles/d41586-021-00097-w…

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38 Ontologies - effective data sharing 31:43

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31:43

Dr Emma Griffiths and Dr João Carriço join us for part two of our crash course on ontologies with a focus on effective data sharing.

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37 Ontologies - the secret sauce of bioinformatics 24:46

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24:46

Dr Emma Griffiths and Dr João Carriço join us to give us a crash course on ontologies, the bioinformatics secret sauce that makes all things work well. Microbial genomics data is like the Tower of Babel with public health talking to food regulators talking to agriculture talking to veterinarians talking to healthcare, all with different languages to describe similar things. So how do we get any work done at all? Listen in to why you need ontologies in your life!…

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36 Roary the pangenome pipeline 21:35

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We chat with Andrew about Roary, software for generating a pangenome, and learn about the background to the project, where the name comes from, hidden features and the light hearted FAQ. Paper: https://academic.oup.com/bioinformatics/article/31/22/3691/240757 Software: https://github.com/sanger-pathogens/Roary Documentation: https://sanger-pathogens.github.io/Roary/…

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35 The Wandering Bioinformatician 26:22

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Have you ever wanted to pack in your job and move to the other side of the world? We chat to Phil Ashton on his travels as a bioinformatician, going from the UK to Vietnam to Malawi. We also wander into microbial bioinformatics and his passion for Salmonella and ETEC. Papers mentioned: SNP-sites: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320690/ Genotyphi: https://www.nature.com/articles/ncomms12827/ ETEC lineages: https://www.biorxiv.org/content/10.1101/2020.07.16.203430v1.abstract…

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34 Moving from wet to dry with Phil Ashton 27:34

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27:34

We chat with Phil Ashton about his move from the wet lab into the dry lab to become a bioinformatician, and his experiences with working in public health and in low and middle income countries.

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33 The untrained monkey 33:30

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Someone shows up at your door wanting to get a nature paper in bioinformatics and they only have a week, where do you start? We talk bioinformatics training with Finlay Maguire.

Micro binfie podcast

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32 Looking behind Majora's Mask and nation wide tracking of SARS-CoV-2 genomics 39:16

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Nick Loman, Sam Nicholls and Radosław Popławski join us to discuss building systems to support the analysis of hundreds of thousands of SARS-CoV-2 genomes in the middle of a pandemic, without using Excel. Preprint about MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance: https://doi.org/10.1101/2020.10.06.328328 COGUK website: https://www.cogconsortium.uk/…

Micro binfie podcast

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31 Large scale sequencing of SARS-CoV-2 genomes from one region 53:02

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We chat to Justin O'Grady, Andrew Page and Alison Mather about how they went about sequencing 1500 SARS-CoV-2 genomes from one small region in the UK (Norfolk), and how they went about using the data for genomic epidemiology to help get a detailed, near real-time view of the pandemic as it unfolded. Some of the key points are that in Norfolk and surrounding regions: 100 distinct UK lineages were identified. 16 UK lineages found in key workers were not observed in patients or in community care. 172 genomes from SARS-CoV-2 positive samples sequenced per 100,000 population representing 42.6% of all positive cases. SARS-CoV-2 genomes from 1035 cases sequenced to a high quality. Only 5 countries, out of 103, have sequenced more SARS-CoV-2 genomes than have been sequenced in Norfolk for this paper. Samples covered the entire first wave, March to August 2020. Stable evolutionary rate of 2 SNPs per month. D614G mutation is the dominant genotype and associated with increased transmission. No evidence of reinfection in 42 cases with longitudinal samples. WGS identified a sublineage associated with care facilities. WGS ruled out nosocomial outbreaks. Rapid WGS confirmed the relatedness of cases from an outbreak at a food processing facility. The manuscript is available from: https://www.medrxiv.org/content/10.1101/2020.09.28.20201475v1…

Micro binfie podcast

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30 How we made the podcast on our 1st birthday 37:25

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To help us celebrate a full year of the podcast after our first episode on September 19, 2019, we go into how we started the podcast. We talk about all aspects including how we met, why we started it, and then how we actually started it.

Micro binfie podcast

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29 Mashtree software deep dive 19:12

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Paper: https://joss.theoj.org/papers/10.21105/joss.01762 Repository: https://github.com/lskatz/mashtree We chat to the author of Mashtree, bioinformatics software for creating a very fast tree from genomes. Citation Katz et al., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762, https://doi.org/10.21105/joss.01762…

Micro binfie podcast

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28 BRIG the BLAST Ring Image Generator 22:17

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We chat to Nabil-Fareed Alikhan about the bioinformatics software he authored called BRIG, the BLAST Ring Image Generator. Software: http://brig.sourceforge.net/ Paper: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402

Micro binfie podcast

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27 SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments 13:46

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We chat to the author of SNP-sites, bioinformatics software for extracting SNPs from a multi-FASTA alignment. Sounds simple but behind all of our software are quirky details that never make it into the final paper. Software: https://github.com/sanger-pathogens/snp-sites Paper: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056 "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)…

Micro binfie podcast

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11 Phylogenetics with the arborists part 1 23:30

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11 Phylogenetics with the arborists part 1 by Microbial Bioinformatics

Micro binfie podcast

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10 History of file formats 40:21

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40:21

10 History of file formats by Microbial Bioinformatics

Micro binfie podcast

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09 Nobel prize or contamination 39:53

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Have you made a nobel prize winning discovery, or are you just looking at contamination. We discuss common sources of contamination in genome sequencing, covering both short and long reads.

Micro binfie podcast

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08 Looking back at 2019 36:16

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So it's the end of 2019 and we thought we'd like to pause and look back at what we were working on . What resonated with us and where we think the micro binfie field will go in the new year.

Micro binfie podcast

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07 Wham, BAM, thank you SAM. 33:40

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This episode we discuss the ubiquitous Sequence Alignment Map (SAM)format

Micro binfie podcast

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Micro binfie podcast

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01 What bioinformatics software not to write part 1 23:52

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In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of genome assembly, read mapping and phylogenetics. Question and comments? microbinfie@gmail.com SHOW NOTES Generally, novel software is not needed if: There are a plethora of existing tools The problem is more or less solved or its been shown to be unsolvable The underlying technology or problem is now obsolete and/or superceded by other methods. Multiple sequence aligners: MAFFT https://mafft.cbrc.jp/alignment/software/ MUSCLE https://www.drive5.com/muscle/ Whole genome aligners: Mauve http://darlinglab.org/mauve/mauve.html Mugsy http://mugsy.sourceforge.net/ Sibellia http://bioinf.spbau.ru/sibelia Parsnp https://github.com/marbl/parsnp Assemblers: SPADES https://github.com/ablab/spades Skesa https://github.com/ncbi/SKESA Velvet https://www.ebi.ac.uk/~zerbino/velvet/ Abyss https://github.com/bcgsc/abyss Edena http://www.genomic.ch/edena.php Ray http://denovoassembler.sourceforge.net/ Long read assemblies HGAP https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-2.0 Flye https://github.com/fenderglass/Flye Canu https://github.com/marbl/canu Ra https://www.biorxiv.org/content/10.1101/656306v1 Unicycler https://github.com/rrwick/Unicycler Read mapping BWA http://bio-bwa.sourceforge.net/ Bowtie2 http://bio-bwa.sourceforge.net/ Minimap2 https://github.com/lh3/minimap2 (BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa) BBtools https://jgi.doe.gov/data-and-tools/bbtools/ BLAST/BLAT: https://genome.ucsc.edu/FAQ/FAQblat.html SMALT https://www.sanger.ac.uk/science/tools/smalt-0 Snippy https://github.com/tseemann/snippy Phenix: https://github.com/phe-bioinformatics/PHEnix Variant callers GATK: https://software.broadinstitute.org/gatk/ VIPR: https://www.viprbrc.org/brc/home.spg?decorator=vipr Varscan2 http://varscan.sourceforge.net/ Workflow managers Bespoke example https://github.com/VertebrateResequencing/vr-codebase Snakemake. https://snakemake.readthedocs.io/en/stable/ Nextflow https://www.nextflow.io/ Galaxy https://usegalaxy.org/ Bpipe https://github.com/ssadedin/bpipe Phylogenetics: Raxml - Raxml-NG https://cme.h-its.org/exelixis/software.html IQTREE http://www.iqtree.org/ FastTree http://www.microbesonline.org/fasttree/ BEAST 1&2 https://www.beast2.org/ RevBayes https://revbayes.github.io/ Metagenomics Taxonomic classification: Megan, Kraken, SIGMA, MIDAS, metaphlan2, mOTUs. Assemblers: MetaSpades, metaflye, MEGAHIT, MetaVelvet, a lot of single isolate assemblers have been tweaked to run on metagenomes. https://github.com/lskatz/Kalamari AMR https://github.com/arpcard/amr_curation https://food-safety-bioinformatics-hackathon.github.io/AMR-protocols/ ABRICATE https://github.com/tseemann/abricate ARIBA https://www.sanger.ac.uk/science/tools/ariba Too many detection tools: https://docs.google.com/spreadsheets/d/18XGWpDiaE249qQKDAL7gdBCka0Z1drpA_s3FElfMJe0/edit#gid=0 Other mentioned resources Mentioned Recent review. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B (2011) A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS ONE 6(3): e17915. https://doi.org/10.1371/journal.pone.0017915 The Assemblerthon: https://assemblathon.org/ Blog post describing that BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa The science web: https://thescienceweb.wordpress.com/2015/03/23/each-bioinformatician-to-have-their-own-personal-short-read-aligner-by-2016/…

Micro binfie podcast

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00 Trailer 0:51

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