Micro binfie podcast

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