antimicrobial resistance clinical microbiology computing distributed computing grants


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.

By Philip Fowler

Philip W Fowler is a computational biophysicist studying antimicrobial resistance working at the John Radcliffe Hospital in Oxford.

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