Micro binfie podcast

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 SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)

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 to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.

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.

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 information from: https://www.cogconsortium.uk/

If you want to access the sequencing data produced by Quadram, please checkout the ENA and GISAID.

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.