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 print: Epidemiological cutoff values for a 96-well broth microdilution plate for M. tuberculosis 5th March 202122nd March 2021 In this preprint, the CRyPTIC project proposes the maximum value of minimum inhibitory concentration (MIC)… 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
Updated preprint: A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology 23rd January 202528th January 2025 In August 2022 seven laboratories across the world uploaded their SARS-CoV-2 genetics files for processing… 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 Can medical microbiology become a big data science? Lessons from CRyPTIC 11th March 202511th March 2025 The CRyPTIC project ran from 2017 to around 2022 and in that time collected over… 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