Micro binfie podcast

Micro binfie podcast

By Microbial BioinformaticsScience
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Micro binfie podcast episodes

  • 57 StaPH-B - Docker containers for Public Health bioinformatics Part 1
    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/
    36 min
  • 56 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2
    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
    26 min
  • 55 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995
    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
    30 min
  • 53 SARS-CoV-2 surveillance in Canada with 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
    34 min
  • 52 SARS-CoV-2 sequencing in Denmark with Mads Albertsen
    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
    29 min
  • 51 SARSCOV2 Round-up 3 and updates from Denmark
    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
    34 min
  • 50 Atypical invasive non-typhoidal Salmonella in The Gambia
    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
    41 min
  • 49 SARS-CoV-2 Tools and resources update
    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
    33 min

About Micro binfie podcast

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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.

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