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Predicting antibiotic resistance de novo

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.

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