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
antimicrobial resistance New paper: predicting pyrazinamide resistance 20th March 202420th March 2024 This paper has finally been published and you can find it here. It had a… 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 preprint: rapid prediction of AMR by free energy methods 15th January 202015th January 2020 The story behind this preprint goes back to the workshop on free energy methods run… 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 publication: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of M. tuberculosis 26th October 2018 In this Microbiology paper we show how a Python package, called the Automated Mycobacterial Detection Growth… 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