GPAS Philip Fowler, 17th May 202113th October 2021 I’ve been working on this for the last few months and very happy that we can now share our plans. Through a very generous donation by ORACLE, a group of researchers led by ModMedMicro at Oxford, are developing a cloud-based clinical microbiology genetics processing service, called the Global Pathogen Analysis System (GPAS). GPAS is still in development and and uses the Scalable Pathogen Processing Pipeline to run a range of bioinformatic workflows on the ORACLE Cloud. For SARS-CoV-2, the idea is you’ll be able to upload SARS-CoV-2 genetic reads* to the ORACLE cloud which will then produce a consensus genome and associated relevant information, for example what lineage does this sample belong to and what mutations are there in the Spike protein? A key principle is that the data is owned by the submitter and therefore submitters will be able to request that their consensus sequence is automatically deposited in a public archive or that their genetic reads are deleted from the cloud following processing. Looking forward to sharing more on this soon. after personal identifiable information has been removed, as is standard. To begin with we will focussing on the ARTIC protocols and Illumina and ONT sequencing. 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 antimicrobial resistance clinical microbiology computing distributed computing grants
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
antimicrobial resistance New preprint: compensatory mutations are associated with increased growth in resistant samples of M. tuberculosis. 22nd June 20238th December 2023 In this preprint, Viki Brunner shows how, using the large CRyPTIC dataset, she can recapitulate… 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: Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex 9th March 202016th March 2020 Although the population structure M. tuberculosis is clonal, one must be careful when inferring the… 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