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
clinical microbiology Our World in Data 10th January 202410th January 2024 I didn’t know that Our World in Data was also based at the University of… 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
New preprint: a deep learning model that can read 96-well broth micro dilution plates 23rd February 202523rd February 2025 The CRyPTIC project used bespoke 96-well broth microdilution plates to measure the minimum inhibitory concentrations… 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 AMyGDA now available from GitHub 27th January 202027th January 2020 AMyGDA is a python module that analyses photographs of 96-well plates and, by examining each… 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