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: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related clinical microbiology gpas
GPAS stopover on the ORACLE road trip 1st February 20221st February 2022 You can listen to Philip Fowler talk about the Global Pathogen Analysis System (GPAS) as… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New paper: quantitative measurement of effect of mutations on antibiotics in M. tuberculosis 15th January 202415th January 2024 The CRyPTIC project played a major role in the release by the WHO of their… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
clinical microbiology New publication: Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers 13th January 202113th January 2021 A second Covid-19 publication I’m proud to be (a small) part of has recently published… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More