51 episodios

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 and Dr. Andrew Page both from Quadram Institute Bioscience (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 or Quadram Institute Bioscience.

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

Micro binfie podcas‪t‬ Microbial Bioinformatics

    • Ciencia

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 and Dr. Andrew Page both from Quadram Institute Bioscience (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 or Quadram Institute Bioscience.

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

    50 Atypical invasive non-typhoidal Salmonella in The Gambia

    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

    • 40 min
    49 SARS-CoV-2 Tools and resources update

    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

    • 32 min
    48 SARS-CoV-2 More Variants of Concern and updates from Africa

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

    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

    • 28 min
    47 SARS-CoV-2 Rapid roundup and questions answered

    47 SARS-CoV-2 Rapid roundup and questions answered

    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

    • 32 min
    46 SARS-CoV-2 genomics resources

    46 SARS-CoV-2 genomics resources

    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

    • 23 min
    45 Software deep dive: Enterobase

    45 Software deep dive: Enterobase

    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)

    • 20 min

Top podcasts en Ciencia

Otros usuarios también se han suscrito a