We talk to Dr Emma Griffiths (UBC), Dr Ruth Timme (FDA) and Dr Duncan MacCannell (CDC) about the PHA4GE SARS-CoV-2 contextual data specification for open genomic epidemiology. Paper: https://www.preprints.org/manuscript/202008.0220/v1 Specification: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification Protocols: https://www.protocols.io/workspaces/pha4ge The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working ...
Aug 13, 2020•38 min
How do you make bioinformatics software sustainable so that we can move our field from academic research into hospitals and doctors offices? We discuss the nuts and bolts of making sustainable bioinformatics software and changes you can make in your own practices: Documentation, Coding styles, Versioning, SOPs and capturing institutional knowledge, Software licencing, Automated testing, Measuring your impact, and going the commercial route.
Jul 30, 2020•27 min
Experimental projects lead to experimental software. We discuss the issues around the sustainability of academic bioinformatics software. How it currently works, why software dies, quality issues, and what we can do to keep it going.
Jul 16, 2020•20 min
We chat with the authors of CoronaHiT which lets you sequence up to 94 SARS-CoV-2 samples on a single MinION flowcell. This reduces the cost of sequencing 3-fold, with a simpler, faster protocol. Justin O'Grady and David Baker join Andrew Page and Nabil-Fareed Alikhan to chat about how it all works, how it came into being and why its awesome. Preprint: https://doi.org/10.1101/2020.06.24.162156
Jul 02, 2020•29 min
When you get an assembly the fun doesnt stop there. You then have to fix it up and see how good it is. In this episode we discuss scaffolding, gapfilling, polishing, assembly metrics, quality control, genome structure, and visualisation tools. Tools and papers mentioned: https://github.com/quadram-institute-bioscience/socru https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004446
Jun 25, 2020•32 min
We chat to Justin O'Grady and Andrew Page on how to get a SARS-CoV-2 sequencing effort off the ground in the middle of a pandemic and go on to sequence 1,500 genomes in 2 months. The Quadram institute is one of 16 sequencing centres in the UK which are part of the COVID-19 genome sequencing consortium. Things we touch off include COG, contamination issues, the people, and bioinformatics. Further information from: https://www.cogconsortium.uk/ If you want to access the sequencing data produced by...
Jun 16, 2020•29 min
Preprocessing of sequence data in advance of de novo assembly is a critical step to improving the final quality of your assembly. We chat about read trimming, correction and filtering, collectively called 'Read Healing'. Software mentioned: https://github.com/sanger-pathogens/plasmidtron
Jun 11, 2020•17 min
Short read de novo assembly is discussed in this podcast. We cover the history of assembly and how short read assemblers have evolved into what we use today. The main focus is on bacterial assembly.
May 28, 2020•25 min
A panel discussion held in MRC Gambia at The London School of Hygiene and Tropical Medicine, recorded in front of a live audience of scientists in January 2020, when SARS-CoV-2 was just beginning to be reported as an emerging infectious disease. The panel consisted of Andrew Page and David Baker from the Quadram Institute, Ozan Gundogdu from LSHTM (UK), Abdul Sesay from LSHTM (Gambia) and Nick Loman from the University of Birmingham and chaired by Suzie Hingley-Wilson from the University of Surr...
May 14, 2020•19 min
The second part of the dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.
Apr 30, 2020•32 min
The dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.
Apr 16, 2020•48 min
We share short war stories about bioinformatics from the trenches of research. We share tales about a mystery massive Listeria outbreak, bubbles on flowcells, GAII woes, contaminated databases, the mass murderer, water pouring into a sequencing centre, changing protocols without validation, Excel issues and the ultimate complexity in science - Humans.
Apr 02, 2020•11 min
Kate Baker talks AMR
Mar 19, 2020•27 min
Someone asks a simple question like "What programming language should I learn?", without realising just how difficult it is to answer. We discuss different programming languages and their use in Bioinformatics.
Mar 05, 2020•30 min
12 Phylogenetics with the arborists part 2 by Microbial Bioinformatics
Feb 20, 2020•32 min
11 Phylogenetics with the arborists part 1 by Microbial Bioinformatics
Feb 06, 2020•24 min
10 History of file formats by Microbial Bioinformatics
Jan 23, 2020•40 min
Have you made a nobel prize winning discovery, or are you just looking at contamination. We discuss common sources of contamination in genome sequencing, covering both short and long reads.
Jan 09, 2020•40 min
So it's the end of 2019 and we thought we'd like to pause and look back at what we were working on . What resonated with us and where we think the micro binfie field will go in the new year.
Dec 26, 2019•36 min
This episode we discuss the ubiquitous Sequence Alignment Map (SAM)format
Dec 12, 2019•34 min
Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prokka, Snippy, Barrnap, Abricate, Shovill, and Nullarbor. Links: https://github.com/tseemann
Nov 28, 2019•44 min
Modern genotyping is discussed in this second part.
Nov 14, 2019•24 min
Genotyping is at the foundation of modern microbiology. We discuss all of the techniques used in the preNGS era.
Oct 31, 2019•29 min
FASTQ files are the foundation of modern bioinformatics. Tune into an informal chat between Lee, Nabil and Andrew as they tell the story of how FASTQs evolved out of nowhere, with all the backstories and qwerks. You might even learn something.
Oct 17, 2019•18 min
In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of metagenomics and anti microbial resistance. Question and comments? microbinfie@gmail.com SHOW NOTES Generally, novel software is not needed if: There are a plethora of existing tools The problem is more or less solved or its been shown to b...
Oct 03, 2019•21 min
In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of genome assembly, read mapping and phylogenetics. Question and comments? microbinfie@gmail.com SHOW NOTES Generally, novel software is not needed if: There are a plethora of existing tools The problem is more or less solved or its been shown...
Sep 19, 2019•24 min
The Micro Binfie poscast is available at SoundCloud (https://soundcloud.com/microbinfie) or you can subscribe via iTunes: https://podcasts.apple.com/au/podcast/microbinfie-podcast/id1479852809 or Spotify: https://podcasters.spotify.com/podcast/2zuzT8EVxbU0yOGFDVareK or your favourite podcast software.
Sep 17, 2019•51 sec
