New preprint: processing 3.9 million SARS-CoV-2 samples to make a consistent phylogenetic tree Philip Fowler, 7th May 20247th May 2024 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:TwitterBlueskyEmailLinkedInMastodon Related clinical microbiology gpas
antimicrobial resistance Postdoctoral position advertised 17th May 202117th May 2021 Through the CompBioMed2 EU Centre of Excellence project I have funding to appoint a postdoctoral… Share this:TwitterBlueskyEmailLinkedInMastodon Read More
antimicrobial resistance New publication: Differential occupational risks to healthcare workers from SARS-CoV- 2 2nd July 202022nd August 2020 Very pleased and proud to be included on this manuscript, which has been published in… Share this:TwitterBlueskyEmailLinkedInMastodon Read More
New publication: CRyPTIC Data Compendium 16th August 202216th August 2022 The large and comprehensive dataset of clinical tuberculosis isolates collected by the CRyPTIC project is… Share this:TwitterBlueskyEmailLinkedInMastodon Read More