New preprint: processing 3.9 million SARS-CoV-2 samples to make a consistent phylogenetic tree Philip Fowler, 7th May 20247th May 2024 0 shares Martin Hunt, Zam Iqbal and lots of others have written an epic preprint where they describe their variant caller, viridian, that was written expressly for producing a consensus genome for a virus using tiled amplicon sequencing. We deployed viridian into our cloud-based sequencing platform during the pandemic and several of us are co-authors on the preprint. Rather than just write a straightforward methods paper, they choose to take it a few steps further and download all the publicly available SARS-CoV-2 FASTQ files from the ENA (which was about 3.9 million) and process them with viridian and then build a phylogenetic tree that is missing some of the artefacts that plague the trees if you simply take FASTA files that have been deposited using a range of genetic pipelines. Share this:Twitter Related clinical microbiology gpas
clinical microbiology New preprint: processing SARS-CoV-2 genetics in the cloud 31st January 202431st January 2024 In this preprint, we describe how in July 2022 for two weeks seven sites in… Share this:Twitter Read More
antimicrobial resistance Cheltenham Science Festival 22nd June 20165th August 2018 A bit over a week ago I helped run the Modernising Medical Microbiology stall at… Share this:Twitter Read More
antimicrobial resistance New paper: detecting compensatory mutations in the RNAP of M. tuberculosis 5th February 20245th February 2024 In this paper, by examining testing the association between mutations known to be associate with… Share this:Twitter Read More