Episodes

Every episode of the podcast, newest first. Each title opens a written overview of the episode — who was on, what was discussed, timestamps you can jump to — and each has a link to listen on SoundCloud. New episodes appear on SoundCloud first.

2026

• Episode 155: Ancient problems require ancient solutions - part 1 · 17 September 2026
  What can DNA recovered from bones, teeth and paleofaeces tell us that living samples can’t — and how do you keep modern contamination from drowning out a… Listen on SoundCloud

• Episode 154: Boston women in bioinformatics · 20 August 2026
  Nabil, Andrew, and Lee talk with Liyang Diao and Valisha Shah from the nonprofit organization, Boston Women in Bioinformatics, a community that supports… Listen on SoundCloud

• Episode 153: Seebot · 23 July 2026
  Nabil-Fareed Alikhan explains Seebot’s checks for bioinformatics software, from help text and testing to maintenance and security. Listen on SoundCloud

• Episode 152: Deacon part 2 · 9 April 2026
  Bede Constantinides explains Deacon’s minimizer-based host-read removal, its Rust implementation and the trade-offs between accuracy and privacy. Listen on SoundCloud

• Episode 151: Deacon part 1 · 26 March 2026
  Bede Constantinides explains why host read removal is difficult, where alignment and Kraken2 fall short, and why he moved from Hostile to Deacon. Listen on SoundCloud

• Episode 150: Genomicx · 12 March 2026
  The hosts test AI-built WebAssembly tools for browser-based genomics, from MashTree to consensus calling, and discuss privacy, validation and limits. Listen on SoundCloud

• Episode 149: Bridging AI & Biosciences · 9 February 2026
  A live Bristol panel on AI in biosciences: microscopy, LLM-assisted research, data leakage, validation and interdisciplinary collaboration. Listen on SoundCloud

2025

• Episode 148: NextFlow debate 3 · 13 November 2025
  The hosts weigh Nextflow maintenance, nf-core standards, AI-assisted interpretation and alternatives including Galaxy, WDL, Terra and Snakemake. Listen on SoundCloud

• Episode 147: NextFlow debate 2 · 30 October 2025
  Can Nextflow pipelines move easily between clouds? The hosts debate containers, debugging, restart limits and the learning curve. Listen on SoundCloud

• Episode 146: NextFlow debate 1 · 16 October 2025
  A staged Nextflow debate on AWS and HPC performance, task overhead, spot instances, modular workflows and difficult debugging. Listen on SoundCloud

• Episode 145: Micro binfie Pathoplexus part 2 · 25 September 2025
  Pathoplexus’s first year: community governance, sequence curation, commercial use, mpox data sharing and funding to keep data available. Listen on SoundCloud

• Episode 144: Micro binfie Pathoplexus part 1 · 11 September 2025
  How Pathoplexus shares viral genomes, protects publication priority and supports outbreak responses with Nextclade, APIs and links to INSDC. Listen on SoundCloud

• Episode 143: Where we catch up on our professional lives · 28 August 2025
  Andrew Page discusses cancer diagnostics, Nabil-Fareed Alikhan updates on Oxford, and Lee Katz explains a change in podcast identity. Listen on SoundCloud

• Episode 142: Genomeqc · 7 August 2025
  Nabil-Fareed Alikhan explains species-specific genome QC thresholds, machine-learning outlier removal and the limits of Illumina-based assemblies. Listen on SoundCloud

• Episode 140: Exploring Clinical Metagenomics · 3 July 2025
  How clinical metagenomics supports difficult diagnoses, from host DNA and noisy databases to clinical interpretation and genomic training. Listen on SoundCloud

• Episode 139: Lassa virus genomics · 19 June 2025
  Sara Zufan discusses Lassa virus diversity, wastewater surveillance in Liberia, and combining laboratory work with bioinformatics. Listen on SoundCloud

• Episode 138: Decoding Tetracycline Resistance in MRSA · 16 January 2025
  Megan Phillips discusses pT181, tetK and variable tetracycline resistance in Staphylococcus aureus, using public genomes and historical papers. Listen on SoundCloud

• Episode 137: Contagion part 2 · 2 January 2025
  Contagion’s genome dashboard, phylogenetic trees and CDC scenes get a bioinformatics review, from R0 claims to early sequencing technology. Listen on SoundCloud

2024

• Episode 135: Assembling ATCC bacterial strains · 19 December 2024
  Andrew Page and Nikhita Puthuveetil discuss ATCC genome assembly, repetitive viral genomes, strain provenance and changing taxonomy. Listen on SoundCloud

• Episode 141: Hackathon panel · 18 December 2024
  A hackathon panel on cgMLST, Nanopore workflows, complete genomes and the limits of routine analysis in public health. Listen on SoundCloud

• Episode 136: Contagion part 1 · 16 December 2024
  How realistic is Contagion? The hosts examine R0, Nipah-inspired MEV1, genome analysis, BSL-4 containment and the film’s ambiguous portrayal of immunity. Listen on SoundCloud

• Episode 134: Diving into MRSA, Genomics, and Public Health · 5 December 2024
  Brooke Talbot joins Andrew Page to discuss recurrent MRSA infections, within-host resistance and genomic epidemiology in public health. Listen on SoundCloud

• Episode 133: The Role of Bioinformatics in Public Health and Disease Outbreaks · 5 December 2024
  Erin Young discusses bacterial species typing in Utah public health and testing Nanopore reads for antimicrobial resistance gene detection. Listen on SoundCloud

• Episode 132: Unlocking the Secrets of Antimicrobial Resistance in Metagenomes · 21 November 2024
  David Mahoney discusses metagenomic assembly graphs, AMR gene transfer and the trade-off between gene recall and sequence context. Listen on SoundCloud

• Episode 131: Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics · 7 November 2024
  Torsten Seemann discusses plans for Snippy NG, Nanopore and assembly support, Australian genomic surveillance and open-source maintenance. Listen on SoundCloud

• Episode 130: Exploring Genomic Innovation and Machine Learning in Public Health · 25 October 2024
  Tim Dallman discusses Shiga toxin-producing E. coli, pangenome-based machine learning and the metadata needed to predict disease risk. Listen on SoundCloud

• Episode 129: Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit · 11 October 2024
  Robert Petit on Bactopia, human-read filtering, YAML-based typing and the practicalities of public health genomics in Wyoming. Listen on SoundCloud

• Episode 128: Haiti cholera outbreak with Christine Lee and Cynney Walters · 19 September 2024
  Christine Lee and Cynney Walters discuss Haiti’s 2022 cholera outbreak, SNP analysis, antimicrobial resistance and gaps in surveillance. Listen on SoundCloud

• Episode 127: Minimum spanning trees · 5 September 2024
  Lee Katz and Nabil-Fareed Alikhan discuss minimum spanning trees, GrapeTree, outbreak profiles and the limits of reading minimum spanning trees as… Listen on SoundCloud

• Episode 126: Tree viz · 22 August 2024
  Lee Katz and Nabil-Fareed Alikhan compare web-based tree viewers, minimum spanning trees and tools for sharing large microbial datasets. Listen on SoundCloud

• Episode 125: Kostas Konstantinidis returns to talk to us about ANI and metagenomics · 6 June 2024
  Kostas Konstantinidis joins Lee Katz and Andrew Page to discuss soil diversity, Nonpareil, oil-spill microbes and long-read metagenomics. Listen on SoundCloud

• Episode 124: Kostas Konstantinidis talks to us about ANI and metagenomics · 23 May 2024
  Kostas Konstantinidis discusses ANI thresholds, Shigella and Salmonella taxonomy, and SeqCode’s role in naming uncultivated microbes. Listen on SoundCloud

• Episode 123: The Revolution of Hash Databases in cgMLST · 21 March 2024
  Lee Katz and Andrew Page discuss hash-based cgMLST allele naming, collision tests, exact matching and decentralised database standards. Listen on SoundCloud

• Episode 122: GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking · 9 March 2024
  Lee Katz and Andrew Page discuss GAMBIT’s targeted k-mers, species calls, reference databases and public health validation. Listen on SoundCloud

• Episode 121: K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown · 1 February 2024
  Titus Brown explains Sourmash sketches, metagenomic comparisons, sequencing noise and why he builds reusable, open-source bioinformatics software. Listen on SoundCloud

• Episode 120: Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown · 18 January 2024
  Titus Brown explains Sourmash sketches, Branchwater searches across a million metagenomes, and the limits of these tools for public health. Listen on SoundCloud

• Episode 119: The Challenges of Microbial Taxonomy - Conversations with Titus Brown · 4 January 2024
  Titus Brown joins Lee Katz and Andrew Page to discuss sourmash, reference quality and the limits of species assignment in public health. Listen on SoundCloud

2023

• Episode 118: Real bioinformaticians react to Jurassic Park · 21 December 2023
  Bioinformaticians revisit Jurassic Park’s ancient DNA, frog-filled genomes, laboratory scenes and Unix claims, separating science from storytelling. Listen on SoundCloud

• Episode 117: From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions · 7 December 2023
  Titus Brown on his route into bioinformatics, digital normalisation, khmer, sourmash and the practical barriers to scientific data reuse. Listen on SoundCloud

• Episode 116: AI Authorship and Ethics in Academic Publishing for Genomics · 23 November 2023
  Lee Katz and Andrew Page discuss ChatGPT authorship, plagiarism, peer review and the risks of AI-assisted writing in microbial genomics. Listen on SoundCloud

• Episode 115: Write-the: speeding up software development for bioinformatics · 9 November 2023
  Wytamma Wirth discusses write-the, codebase context, constrained AI agents and turning generated docstrings into searchable documentation. Listen on SoundCloud

• Episode 114: Write-the: Automating Code Documentation ChatGPT · 4 November 2023
  Wytamma Wirth explains how write-the uses ChatGPT to generate docstrings and tests, convert code and build a phylogenetic tree library. Listen on SoundCloud

• Episode 113: Global Microbial Identifier conference with Ruth Timme · 18 September 2023
  Ruth Timme joins Lee and Andrew at GMI13 to discuss pathogen genome submissions, metadata standards and international adoption. Listen on SoundCloud

• Episode 112: Global Microbial Identifier conference with Will Hsiao · 17 September 2023
  William Hsiao joins Andrew Page and Lee Katz at GMI13 in Vancouver to discuss equitable data sharing, conference inclusion and interoperability. Listen on SoundCloud

• Episode 111: Global Microbial Identifier with Finlay Maguire and Emma Griffiths · 16 September 2023
  Finlay Maguire and Emma Griffiths join Andrew Page and Lee Katz at GMI 13 to discuss microbial data sharing, One Health and Tim Hortons. Listen on SoundCloud

• Episode 110: ChatGPT: The Bioinformatics Calculator · 6 July 2023
  Can ChatGPT solve bioinformatics exercises? The hosts discuss coding tests, assessment, regular expressions and possible sequencing applications. Listen on SoundCloud

• Episode 109: AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics · 22 June 2023
  Lee, Andrew and Nabil test AI code translation, discuss Copilot workflows and examine convincing errors in bioinformatics content. Listen on SoundCloud

• Encore: What language should I learn? · 8 June 2023
  Python, R or Perl? The hosts compare first languages, established libraries, programming fundamentals and SQL skills for bioinformatics. Listen on SoundCloud

• Episode 108: SeqCode: a nomenclatural code for prokaryotes described from sequence data · 25 May 2023
  Marike Palmer and Miguel Rodriguez explain SeqCode, genome quality standards and the debate over naming uncultivated prokaryotes. Listen on SoundCloud

• Episode 107: Systematics and naming of prokaryotes in the era of sequencing · 11 May 2023
  Marike Palmer and Miguel Rodriguez explain SeqCode, genome-based nomenclatural types and stable names for cultivated and uncultivated prokaryotes. Listen on SoundCloud

• Episode 106: Why on earth would you do a PostDoc? · 27 April 2023
  Three postdocs discuss pay, insecure contracts and academic freedom, including SARS-CoV-2 sequencing in Pakistan and careers in bioinformatics. Listen on SoundCloud

• Episode 105: Mobile genetic elements panel discussion · 20 April 2023
  A live panel on mobile genetic elements, XDR typhoid in Pakistan, staphylococcal resistance and why sequencing still needs laboratory validation. Listen on SoundCloud

• Episode 104: The Kraken software suite · 6 April 2023
  Jennifer Lu and Natalia Rincon explain Kraken’s tools, database trade-offs, pathogen detection and contamination checks. Listen on SoundCloud

• Episode 103: Release the Kraken · 23 March 2023
  Jennifer Lu and Natalia Rincon explain Kraken classification, database choices, memory needs, abundance estimation and low-read pathogen detection. Listen on SoundCloud

• Episode 102: Early days of MLST · 9 March 2023
  Ed Feil and Natacha Couto discuss why MLST uses seven genes, how eBURST changed its analysis, and what sequence types still offer in the genomic era. Listen on SoundCloud

• Episode 101: One Health with Natacha Couto and Ed Feil · 23 February 2023
  Natacha Couto and Ed Feil discuss One Health, AMR transmission, sampling bias and why resistance genes do not always mean resistant bacteria. Listen on SoundCloud

• Episode 100: The 100th episode · 9 February 2023
  The hosts mark 100 episodes with five-year predictions for sequencing, wastewater surveillance, data storage and personalised microbiome medicine. Listen on SoundCloud

• Episode 99: Stories from the frontlines of bioinformatics · 26 January 2023
  PDFs, Excel errors, COVID lab workflows and bacterial quirks: a live panel on the practical problems of microbial bioinformatics. Listen on SoundCloud

• Episode 98: Nomadic bioinformatics with Frank · 12 January 2023
  Frank Ambrosio on moving from CDC laboratory work to Theiagen, cloud bioinformatics, remote mentoring and a travelling working life. Listen on SoundCloud

2022

• Episode 97: Advances in sequencing technologies · 29 December 2022
  The hosts compare Nanopore Q20, adaptive sequencing, PacBio HiFi and Illumina long-read plans, and consider the implications for microbial software. Listen on SoundCloud

• Episode 96: IMMEM XIII and ASM NGS conference roundup · 22 December 2022
  Lee Katz, Andrew Page and Nabil-Fareed Alikhan compare hybrid conferences, real-time wastewater surveillance and genomic metadata. Listen on SoundCloud

• Episode 95: Lost in Translation with Torsten Seemann · 8 December 2022
  Torsten Seemann joins the hosts to compare COVID-19 sequencing, outbreak reporting and data sharing in Australia, the UK and the US. Listen on SoundCloud

• Episode 94: The great scientific Mastodon migration · 17 November 2022
  Nabil-Fareed Alikhan explains the costs and moderation of mstdn.science, while Emma Hodcroft discusses why scientists are trying Mastodon. Listen on SoundCloud

• Episode 93: Roary Troubleshooting And Issues · 10 November 2022
  The hosts work through Roary bug reports, from missing sequences and dependencies to empty core genomes, and explain how to report problems clearly. Listen on SoundCloud

• Episode 92: Avoid dependency hell and get up and running fast · 27 October 2022
  Lee Katz, Andrew Page and Nabil-Fareed Alikhan discuss bioinformatics dependencies, Conda, Mamba and containers for more manageable installations. Listen on SoundCloud

• Episode 91: What language should I learn? · 13 October 2022
  Python, R, Perl or SQL? Lee Katz, Andrew Page and Nabil-Fareed Alikhan discuss where to start and why libraries and local support matter. Listen on SoundCloud

• Episode 90: Public health bioinformatics on the cloud with WDL + Terra.bio · 29 September 2022
  How public health labs use Terra.bio and WDL for SARS-CoV-2 analysis, data sharing and cloud computing without managing their own servers. Listen on SoundCloud

• Episode 89: What do we do with WDL? · 15 September 2022
  Joel and Danny discuss WDL, portable bioinformatics pipelines, and how containers and workflow languages support public health laboratories. Listen on SoundCloud

• Episode 88: Sepia directors cut · 4 August 2022
  Henk den Bakker explains Sepia, a Rust read classifier, covering taxonomy, batch processing, memory use and food-safety metagenomics. Listen on SoundCloud

• Episode 87: Nextstrain, SARSCOV2 and dealing with a data deluge · 21 July 2022
  Emma Hodcroft and Leonardo de Oliveira Martins discuss Nextstrain, SARS-CoV-2 downsampling, data quality and the CoVariants website. Listen on SoundCloud

• Episode 86: What’s next for nextstrain? · 7 July 2022
  Emma Hodcroft explains Nextstrain, Augur, Auspice and the challenges of adapting viral phylogenetic tools to bacterial genomes. Listen on SoundCloud

• Episode 85: Breaking the dogma with bioinformatics · 23 June 2022
  Mark Pallen on outbreak genomics, the 2011 German E. coli outbreak, ancient TB and the microbial diversity still hidden in metagenomes. Listen on SoundCloud

• Episode 84: Bioinformatics in the noughties with Mark Pallen · 9 June 2022
  Mark Pallen recalls PSI-BLAST, sortases, ESAT-6 and E. coli, showing how early microbial genomes challenged assumptions about bacterial biology. Listen on SoundCloud

• Episode 83: A short journey into mobile genetic elements · 26 May 2022
  Why bacterial mobile genetic elements are hard to assemble and annotate, with examples from Vibrio, E. coli, pertussis and Shigella. Listen on SoundCloud

• Episode 82: Bioinformatics moments before the millennium · 12 May 2022
  Mark Pallen recalls manual protein assembly, H. pylori urease, early PCR experiments and analysing the first Campylobacter jejuni genome. Listen on SoundCloud

• Episode 81: The people behind the benchmark datasets for SARS-CoV-2 · 29 April 2022
  Lingzi Xiaoli and Jill Hagey explain how they mined SARS-CoV-2 data, checked SRA metadata and selected benchmark samples against CDC references. Listen on SoundCloud

• Episode 80: Benchmark datasets for SARS-CoV-2 · 28 April 2022
  Lingzi Xiaoli and Jill Hagey explain SARS-CoV-2 benchmark datasets for pipeline validation, lineage testing and failed quality-control scenarios. Listen on SoundCloud

• Episode 79: StaPH-B: Stable containers for public health bioinformatics · 14 April 2022
  Erin Young and Kelsey Florek explain StaPH-B containers, workflow validation and simpler ways to run public health bioinformatics. Listen on SoundCloud

• Episode 78: StaPH-B: state public health bioinformatics · 31 March 2022
  Erin Young and Kelsey Florek discuss StaPH-B, the Cecret SARS-CoV-2 pipeline and the challenges of scaling public health bioinformatics. Listen on SoundCloud

• Episode 77: Genomics for a new era · 17 March 2022
  Zamin Iqbal and Grace Blackwell discuss searchable bacterial assemblies, mobile elements, AMR genes and the biases in public sequencing data. Listen on SoundCloud

• Episode 76: What are the major challenges for getting AMR genomics into the clinic? · 3 March 2022
  A panel examines clinical AMR genomics: prediction accuracy, mixed infections, accreditation, reporting, costs and infection control. Listen on SoundCloud

• Episode 74: SEPIA With Henk - Soup Or Salad Yes! · 3 February 2022
  Henk discusses SEPIA, a Rust read classifier, with batch processing, flexible taxonomies and applications in food safety metagenomics. Listen on SoundCloud

• Episode 73: Bactopia and using workflow managers in bioinformatics part 2 · 20 January 2022
  Robert Petit discusses workflow managers, Prokka and containers, and when custom bioinformatics scripts should become reproducible workflows. Listen on SoundCloud

• Episode 72: Bactopia and using workflow managers in bioinformatics part 1 · 6 January 2022
  Robert Petit explains how Bactopia processes bacterial genomes, separates isolate analysis from comparative genomics, and builds on Nextflow. Listen on SoundCloud

2021

• Episode 70: Bacterial Taxonomy: the grand vista is ahead of us · 17 December 2021
  Phil Hugenholtz, Iain Sutcliffe and Mark Pallen discuss GTDB, evolutionary ranks, 16S limits and classifying uncultured bacteria. Listen on SoundCloud

• Episode 71: Bacterial taxonomy: Into the unknown, SeqCode, naming uncultured multitudes and renaming of phyla · 17 December 2021
  Phil Hugenholtz, Iain Sutcliffe and Mark Pallen debate naming uncultured bacteria, SeqCode, GTDB and controversial phylum renaming. Listen on SoundCloud

• Episode 69: Background to bacterial taxonomy · 16 December 2021
  Why bacterial names change: Linnaean classification, phylogeny, naming rules and the case for genome-based taxonomy. Listen on SoundCloud

• Episode 68: Bacterial Taxonomy: what is a species, what is a strain? part 2 · 9 December 2021
  How GTDB, ANI and GenomeRxiv classify bacteria, and why species names, strains and lineages matter for diagnostics and public health. Listen on SoundCloud

• Episode 67: Bacterial Taxonomy: what is a species, what is a strain? · 25 November 2021
  How bacterial species are defined, why ANI matters, and where genome-based taxonomy clashes with clinical names and unculturable microbes. Listen on SoundCloud

• Episode 66: Scholarly Communications for Bioinformaticians · 18 November 2021
  The hosts discuss Google Scholar, ORCID, peer review credit, Twitter and GitHub as practical ways to make bioinformatics work easier to find. Listen on SoundCloud

• Episode 75: How to review a bioinformatics paper in 10 days or less · 2 November 2021
  How to review bioinformatics papers efficiently: check methods, results, code and data, recognise fatal flaws and write useful feedback. Listen on SoundCloud

• Episode 65: Genomics of Mycobacterium tuberculosis · 28 October 2021
  TB genomics, drug resistance and transmission: tools, slow mutation rates, spoligotyping and biological questions sequencing cannot yet answer. Listen on SoundCloud

• Episode 64: Mycobacterium tuberculosis: the forgotten pandemic · 14 October 2021
  Why TB remains a global threat, and how slow growth, mixed infections and drug resistance complicate genomic surveillance and treatment. Listen on SoundCloud

• Episode 63: A dive into Campylobacter genomics · 30 September 2021
  Ozan Gundogdu discusses Campylobacter genomes, phase variation, laboratory passage, plasmids and the case for long-read sequencing. Listen on SoundCloud

• Episode 62: Campylobacter: the fussy little pathogen · 16 September 2021
  Ozan Gundogdu explains Campylobacter transmission, its compact genome, chicken carriage and the challenges of vaccines and disease control. Listen on SoundCloud

• Episode 61: Non FUNGIble tokens: you too can own BRCA1 · 2 September 2021
  The hosts explore genome NFTs, decentralised accession numbers and BioBucks, while Lee Katz explains his $38 BRCA1 image experiment. Listen on SoundCloud

• Encore of episode 6: What software not to write · 1 July 2021
  Torsten Seemann discusses Prokka, reliable command-line tools, Conda packaging and the long-term work of maintaining bioinformatics software. Listen on SoundCloud

• Episode 60: Whats in a name: Salmonella and E. Coli · 17 June 2021
  Why E. coli pathotypes and Salmonella serovars do not neatly match genomes, and what MLST, ANI and in silico serotyping can tell us. Listen on SoundCloud

• Episode 59: Microbe Moment Micro Binfie · 3 June 2021
  Lee, Andrew and Nabil answer the Microbigals’ questions about favourite microbes, fermented foods, cancer research and careers in bioinformatics. Listen on SoundCloud

• Episode 58: StaPH-B careers with Curtis Kapsak and Kevin Libuit · 21 May 2021
  Curtis Kapsak and Kevin Libuit trace their paths from biology to public health, APHL fellowships and cloud-based SARS-CoV-2 analysis. Listen on SoundCloud

• Episode 57: StaPH-B - Docker containers for Public Health bioinformatics Part 1 · 7 May 2021
  Curtis Kapsak and Kevin Libuit explain StaPH-B Docker containers, version control, Pangolin automation and database choices for public health labs. Listen on SoundCloud

• Episode 56: SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2 · 21 April 2021
  Kai Blin and Tue Jorgensen explain a $5 Sanger screen for SARS-CoV-2 variants, its Ct limits and browser-based analysis without data uploads. Listen on SoundCloud

• Episode 55: SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995 · 8 April 2021
  Kai Blin and Tue Jorgensen explain rapid SARS-CoV-2 mutation screening with Sanger sequencing and a tested, portable analysis pipeline. Listen on SoundCloud

• Episode 54: SARS-CoV-2 In Canada and addressing data sharing and privacy · 1 April 2021
  Emma Griffiths, Finn McGuire and William Hsiao discuss SARS-CoV-2 metadata, privacy rules and genomic surveillance in Canada. Listen on SoundCloud

• Episode 53: SARS-CoV-2 surveillance in Canada with CANCOGEN · 25 March 2021
  Emma Griffiths, William Hsiao and Finlay McGuire discuss Canada’s SARS-CoV-2 sequencing, data sharing, analysis workflows and variant surveillance. Listen on SoundCloud

• Episode 52: SARS-CoV-2 sequencing in Denmark with Mads Albertsen · 18 March 2021
  Mads Albertsen explains Denmark’s SARS-CoV-2 sequencing: sample logistics, modified ARTIC protocols, Nanopore capacity and data-sharing limits. Listen on SoundCloud

• Episode 51: SARSCOV2 Round-up 3 and updates from Denmark · 11 March 2021
  Denmark’s SARS-CoV-2 sequencing coverage, emerging variants, public health workflows and practical checks for contamination and sample swaps. Listen on SoundCloud

• Episode 50: Atypical invasive non-typhoidal Salmonella in The Gambia · 25 February 2021
  Abdoulie Kanteh and Grant Mackenzie discuss changing invasive Salmonella serovars in The Gambia, genomics and implications for vaccines. Listen on SoundCloud

• Episode 49: SARS-CoV-2 Tools and resources update · 22 February 2021
  Peter van Heusden joins the hosts to discuss SARS-CoV-2 analysis tools, data sharing, CoronaHiT and benchmarks for public health genomics. Listen on SoundCloud

• Episode 48: SARS-CoV-2 More Variants of Concern and updates from Africa · 20 February 2021
  Peter van Heusden discusses SARS-CoV-2 variants, low-coverage sequencing and the challenges of genomic surveillance in Africa. Listen on SoundCloud

• Episode 47: SARS-CoV-2 Rapid roundup and questions answered · 8 February 2021
  Missing SNPs, E484K, Nanopore basecalling, ARTIC artefacts and genome sharing: practical SARS-CoV-2 analysis advice from February 2021. Listen on SoundCloud

• Episode 46: SARS-CoV-2 genomics resources · 8 February 2021
  A February 2021 roundup of CoVariants, lineage reports, Microreact, training resources and faster ways to track and share SARS-CoV-2 genomes. Listen on SoundCloud

• Episode 45: Software deep dive: Enterobase · 4 February 2021
  How EnteroBase combines bacterial genomes, curated metadata and cgMLST, with lessons on Salmonella sampling bias and finding related isolates. Listen on SoundCloud

• Episode 44: How to sequence SARS-CoV-2 using the ARTIC protocol with Joshua Quick · 22 January 2021
  Joshua Quick explains SARS-CoV-2 sequencing with ARTIC, covering primer design, amplicon dropouts, Nanopore barcoding and data quality. Listen on SoundCloud

• Episode 43: Why use genomics in an epidemic? with Sam Sheppard · 21 January 2021
  Sam Sheppard explains how genome data support outbreak investigation, coronavirus surveillance and global comparisons, and where CLIMB fits in. Listen on SoundCloud

• Episode 42: Overcoming barriers to SARS-CoV-2 data analysis · 20 January 2021
  A panel on SARS-CoV-2 metadata, within-host variation, public health sequencing and validation of ARTIC, Pangolin and Civet workflows. Listen on SoundCloud

• Episode 41: SARS-CoV-2 Phylogenomics questions answered · 19 January 2021
  A January 2021 panel on SARS-CoV-2 outbreak detection, Pangolin lineages, Civet and Llama, contextual genomes and variant-call quality. Listen on SoundCloud

• Episode 40: A crash course in SARS-CoV-2 bioinformatics · 18 January 2021
  How to analyse SARS-CoV-2 amplicon data: established pipelines, missing bases, contamination checks, metadata and public health interpretation. Listen on SoundCloud

• Episode 39: Explaining the naming of SARS-CoV-2 new variants · 16 January 2021
  Andrew Page and Niamh Tumelty discuss SARS-CoV-2 variant names, competing naming schemes and confusion over emerging lineages in January 2021. Listen on SoundCloud

• Episode 38: Ontologies - effective data sharing · 7 January 2021
  Emma Griffiths and João Carriço discuss metadata standards, free-text mapping and the practical limits of ontologies for sharing microbial genomics data. Listen on SoundCloud

2020

• Episode 37: Ontologies - the secret sauce of bioinformatics · 24 December 2020
  Emma Griffiths and João Carriço explain how ontologies clarify microbial metadata, link datasets and give genome analyses their context. Listen on SoundCloud

• Episode 36: Roary the pangenome pipeline · 10 December 2020
  Andrew Page explains Roary’s origins, fast pangenome comparisons, annotation requirements and why quality control matters. Listen on SoundCloud

• Episode 35: The Wandering Bioinformatician · 26 November 2020
  Phil Ashton on bioinformatics in Vietnam and Malawi: metered data, power cuts, Salmonella surveillance and plans for ETEC research. Listen on SoundCloud

• Episode 34: Moving from wet to dry with Phil Ashton · 12 November 2020
  Phil Ashton on moving from wet-lab biology to bioinformatics, Salmonella surveillance, workflow tools and working in Vietnam and Malawi. Listen on SoundCloud

• Episode 33: The untrained monkey · 29 October 2020
  Lee Katz, Andrew Page and Finlay Maguire debate short bioinformatics courses, Galaxy, command-line skills and realistic research goals. Listen on SoundCloud

• Episode 32: Looking behind Majora’s Mask and nation wide tracking of SARS-CoV-2 genomics · 15 October 2020
  Nick Loman, Sam Nicholls and Radosław Popławski explain how Majora links SARS-CoV-2 genomes and metadata across COG-UK. Listen on SoundCloud

• Episode 31: Large scale sequencing of SARS-CoV-2 genomes from one region · 1 October 2020
  How Norfolk sequenced SARS-CoV-2 during the first wave, using ARTIC, lineage analysis and clinical data to investigate local outbreaks. Listen on SoundCloud

• Episode 30: How we made the podcast on our 1st birthday · 17 September 2020
  Lee, Andrew and Nabil explain how MicroBinfie began, from Slack discussions and a six-episode pilot season to microphones, Zoom and Audacity. Listen on SoundCloud

• Episode 29: Mashtree software deep dive · 10 September 2020
  Lee Katz explains how Mashtree builds rapid genome-comparison trees from Mash sketches, and why they are a first pass rather than a phylogeny. Listen on SoundCloud

• Episode 28: BRIG the BLAST Ring Image Generator · 27 August 2020
  Nabil-Fareed Alikhan explains BRIG’s circular genome plots, its beer-wager origins, and the design choices behind its lasting use. Listen on SoundCloud

• Episode 27: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments · 13 August 2020
  Andrew Page explains how SNP-sites extracts variants from alignments, why it reads files twice, and how testing and packaging keep it useful. Listen on SoundCloud

• Episode 26: SARS-CoV-2 contextual data specification for open genomic epidemiology · 13 August 2020
  PHA4GE panellists explain a SARS-CoV-2 metadata specification, repository submissions and how contextual data supports public health surveillance. Listen on SoundCloud

• Episode 25: Sustainable bioinformatics software · 30 July 2020
  The hosts discuss documentation, testing, versioning, licences and funding models for bioinformatics software used in research and public health. Listen on SoundCloud

• Episode 24: Experimental projects lead to experimental software · 16 July 2020
  Lee Katz, Andrew Page and Nabil-Fareed Alikhan discuss short grants, software maintenance and credit for sustainable bioinformatics tools. Listen on SoundCloud

• Episode 23: CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes on Nanopore · 2 July 2020
  Justin O’Grady and David Baker explain CoronaHiT, a lower-cost method for multiplexing up to 94 SARS-CoV-2 samples on a Nanopore flow cell. Listen on SoundCloud

• Episode 22: Assembly after party · 25 June 2020
  Checking microbial genome assemblies with read mapping, polishing, QUAST, socru and genome viewers—and why N50 alone is not enough. Listen on SoundCloud

• Episode 21: Setting up coronavirus sequencing for real-time public health surveillance · 16 June 2020
  Justin O’Grady and Andrew Page explain how Quadram set up SARS-CoV-2 sequencing, from ARTIC PCR and contamination to COG-UK data sharing. Listen on SoundCloud

• Episode 20: Assembly read healing · 11 June 2020
  How trimming, correction and filtering affect genome assembly, and why duplicate reads, uneven coverage and plasmids need care. Listen on SoundCloud

• Episode 19: Microbinfies assemble · 28 May 2020
  How bacterial short-read assemblers evolved, and how Velvet, SPAdes, Shovill and SKESA compare on speed, accuracy and reproducibility. Listen on SoundCloud

• Episode 18: Panel - Has Nanopore rendered onsite Illumina obsolete? · 14 May 2020
  A January 2020 panel in The Gambia weighs Nanopore against Illumina for outbreaks, metagenomics, sequencing access and data ownership. Listen on SoundCloud

• Episode 17: Bayesian magic in practice · 30 April 2020
  Practical Bayesian phylogenetics: learning RevBayes, checking MCMC convergence, comparing clock models and testing priors and sampling dates. Listen on SoundCloud

• Episode 16: The theory behind Bayesian Magic · 16 April 2020
  Nabil-Fareed Alikhan, Conor Meehan and Leo Martins discuss Bayesian phylogenetics, MCMC, uncertainty and reproducible analyses. Listen on SoundCloud

• Episode 15: Bioinformatics war stories · 2 April 2020
  The hosts recount Listeria pseudo-outbreaks, flow cell faults, contaminated reference databases, Excel mix-ups and a flooded sequencing facility. Listen on SoundCloud

• Episode 14: La resistance lives on: The AMR deep dive · 19 March 2020
  Kate Baker discusses Shigella resistance, ResFinder, plasmid context, long reads and why genomic predictions need more than gene detection. Listen on SoundCloud

• Episode 13: Questions not to ask · 5 March 2020
  The hosts compare Perl, Python and newer languages for bioinformatics, weighing readable code, performance, community support and maintenance. Listen on SoundCloud

• Episode 12: Phylogenetics with the arborists part 2 · 20 February 2020
  Conor Meehan and Leonardo de Oliveira Martins discuss evolutionary models, recombination, SNP bias and whole-genome phylogenetics. Listen on SoundCloud

• Episode 11: Phylogenetics with the arborists part 1 · 6 February 2020
  Conor Meehan and Leonardo de Oliveira Martins discuss phylogenetic methods, core-genome bias, alignment checks and misleading branch lengths. Listen on SoundCloud

• Episode 10: History of file formats · 23 January 2020
  Why bioinformatics has so many file formats: FASTQ, BAM, genome annotation, BLAST outputs and the practical headaches of parsing and conversion. Listen on SoundCloud

• Episode 9: Nobel prize or contamination · 9 January 2020
  How to spot contamination in microbial sequencing with taxonomic checks, assembly metrics and controls, and recognise short- and long-read failures. Listen on SoundCloud

2019

• Episode 8: Looking back at 2019 · 26 December 2019
  A review of 2019’s microbial bioinformatics tools, from Kraken2 and GTDB to long-read assembly, containers and browser-based analysis. Listen on SoundCloud

• Episode 7: Wham, BAM, thank you SAM. · 12 December 2019
  How SAM, BAM and CRAM store read alignments, with samtools workflows, clipping, genome viewers and the case for long-term software support. Listen on SoundCloud

• Episode 6: Writing good bioinformatics software with Torsten Seemann · 28 November 2019
  Torsten Seemann discusses Prokka, standard formats, Conda packaging and the long-term work of maintaining useful bioinformatics software. Listen on SoundCloud

• Episode 5: History of Genotyping - Decentralised Future · 14 November 2019
  Lee Katz, Andrew Page and Nabil-Fareed Alikhan discuss genomic metadata, patient privacy and locally run pipelines for global surveillance. Listen on SoundCloud

• Episode 4: History of Genotyping - The early years · 31 October 2019
  How PFGE, MLST, MLVA and older typing methods shaped outbreak surveillance, and how PulseNet, GenomeTrakr and Galaxy support shared analysis. Listen on SoundCloud

• Episode 3: FASTQ - all your bases are belong to us · 17 October 2019
  FASTQ quality scores, compression, read ordering and parsing traps: the hosts discuss the everyday format behind microbial sequencing analysis. Listen on SoundCloud

• Episode 2: What bioinformatics software not to write part 2 · 3 October 2019
  The hosts question new metagenomics and AMR tools, arguing for better databases, long-read methods, useful visualisation and easier installation. Listen on SoundCloud

• Episode 1: What bioinformatics software not to write part 1 · 19 September 2019
  When should you avoid writing another assembler, mapper or variant caller? The hosts discuss mature tools, data quality and reinventing the wheel. Listen on SoundCloud

• Episode 0: Trailer · 17 September 2019
  Meet hosts Lee Katz, Andrew Page and Nabil-Fareed Alikhan, and hear plans for conversations about microbial bioinformatics. Listen on SoundCloud