SARS-CoV-2 pipeline live on EIT Pathogena Philip Fowler, 28th January 202528th January 2025 Back in the SARS-CoV-2 pandemic we worked closely with ORACLE Corp to build and deploy a bioinformatics pipeline in ORACLE Cloud that processes raw genetic files and infers what the consensus genome is and hence what lineage (e.g. BA.2) it belongs to. The heart of the pipeline is an amplicon-aware variant caller, viridian, that was written by Zamin Iqbal’s group and there is a nice preprint out showing how it avoids various calling artefacts that can complicate phylogenetic tree construction. An improved version of the pipeline has now been deployed, tested and launched on EIT Pathogena, a cloud-based genetics platform. Anyone can sign up and process at least 1,000 samples for free. 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
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 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
antimicrobial resistance New preprint: rapidly and reproducibly building resistant catalogues for M. tuberculosis 3rd October 202530th October 2025 The CRyPTIC project carried out many exciting research projects but it never quite got around… 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