SARS-CoV-2 bioinformatics

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

54 SARS-CoV-2 In Canada and addressing data sharing and privacy

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

56 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2

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

55 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.  Find out more at https://github.com/CDCgov/datasets-sars-cov-2

* Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/
* Jill can be found on Twitter at @JillHagey and jvhagey.github.io
* Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/

80 Benchmark datasets for SARS-CoV-2

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.  Find out more at https://github.com/CDCgov/datasets-sars-cov-2.  See our previous episode for part 1 of the conversation.

* Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/
* Jill can be found on Twitter at @JillHagey and jvhagey.github.io
* Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/

81 The people behind the benchmark datasets for SARS-CoV-2

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

49 SARS-CoV-2 Tools and resources update

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 from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (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, University of Oxford or Theiagen Genomics.

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

49 SARS-CoV-2 Tools and resources update

Micro Binfie Podcast