Episodes

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.

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.

In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician.

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. See our previous episode for part 1 of the conversation.

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.

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!

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.

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

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.

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

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

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.

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.

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/Micro Binfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/ Taxonomy_Selective_bibliography.pdf

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.

We’re navigating the twisted world of bacterial taxonomy. We have some excellent guides to help us!

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

We’re navigating the twisted world of bacterial taxonomy. We have some excellent guides to help us!

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.

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.

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.

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.

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.

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

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

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

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

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

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

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

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/

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

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

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

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

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

We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Mads Albertsen and the latest developments in Denmark.

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

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: ht tps://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-008 39-5

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

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

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

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)

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

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/

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

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/

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

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

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.

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!

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/

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

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.

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.

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/

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

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.

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

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

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/10.10 99/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)

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.

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.

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.

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

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

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.

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

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.

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.

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

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

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.

Kate Baker talks AMR

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.

12 Phylogenetics with the arborists part 2 by Microbial Bioinformatics

11 Phylogenetics with the arborists part 1 by Microbial Bioinformatics

10 History of file formats by Microbial Bioinformatics

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.

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.

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

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.

Modern genotyping is discussed in this second part.

Genotyping is at the foundation of modern microbiology. We discuss all of the techniques used in the preNGS era.

FASTQ files are the foundation of modern bioinformatics. Tune into an informal chat between Lee, Nabil and Andrew as they tell the story of how FASTQs evolved out of nowhere, with all the backstories and qwerks. You might even learn something.

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 metagenomics and anti microbial resistance.

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.

The Micro Binfie podcast is available at SoundCloud (https://soundcloud.com/microbinfie)