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
Apr 21, 2021•25 min
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....
Apr 08, 2021•29 min
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
Apr 01, 2021•26 min
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
Mar 25, 2021•33 min
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
Mar 18, 2021•29 min
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.or...
Mar 11, 2021•34 min
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
Feb 25, 2021•41 min
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 ht...
Feb 22, 2021•33 min
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/vari...
Feb 20, 2021•29 min
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 ...
Feb 08, 2021•33 min
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-...
Feb 08, 2021•24 min
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 htt...
Feb 04, 2021•21 min
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
Jan 22, 2021•22 min
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/
Jan 21, 2021•19 min
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...
Jan 20, 2021•47 min
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 yo...
Jan 19, 2021•25 min
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
Jan 18, 2021•57 min
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 n...
Jan 16, 2021•20 min
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.
Jan 07, 2021•32 min
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!
Dec 24, 2020•25 min
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/
Dec 10, 2020•22 min
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
Nov 26, 2020•26 min
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.
Nov 12, 2020•28 min
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.
Oct 29, 2020•34 min
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/
Oct 15, 2020•39 min
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. 1...
Oct 01, 2020•53 min
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.
Sep 17, 2020•37 min
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
Sep 10, 2020•19 min
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
Aug 27, 2020•22 min
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, Torst...
Aug 13, 2020•14 min
