Micro binfie podcast

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

We chat to Nabil-Fareed Alikhan about the bioinformatics software he authored called BRIG, the BLAST Ring Image Generator. Software: http://brig.sourceforge.net/ Paper: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402

We chat to the author of SNP-sites, bioinformatics software for extracting SNPs from a multi-FASTA alignment. Sounds simple but behind all of our software are quirky details that never make it into the final paper. Software: https://github.com/sanger-pathogens/snp-sites Paper: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056 "SNP-sites: rapid efficient extraction of...

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 fo...

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...

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.

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

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

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 i...

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

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.

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 Lom...

The second part of the dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.

The dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.

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.

Kate Baker talks AMR

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.

12 Phylogenetics with the arborists part 2 by Microbial Bioinformatics

11 Phylogenetics with the arborists part 1 by Microbial Bioinformatics

10 History of file formats by Microbial Bioinformatics

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.

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.

This episode we discuss the ubiquitous Sequence Alignment Map (SAM)format

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

Modern genotyping is discussed in this second part.