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Genomic pathogen surveillance using Nextflow on AWS

The Centre for Genomic Pathogen Surveillance (CGPS) is based at the Wellcome Genome Campus, Cambridge and The Big Data Institute, University of Oxford in the United Kingdom. The Centre hopes to enable the linking and real-time interpretation of data globally to track pathogens and antimicrobial resistance in a cost-effective manner.

Using AWS CloudFormation and AWS Batch with Nextflow, Dr. Anthony Underwood, bioinformatics implementation manager for the Centre for Genomic Pathogen Surveillance and Ben Taylor, senior software engineer, with their colleagues built a solution that allows a new pipeline to be deployed with just a few commands (instructions for using this software can be found online). Nextflow pipelines, coupled with AWS, have the capacity to scale up pipelines and run hundreds or even thousands of jobs in parallel. Now, end users can start a pipeline and monitor it using a web page, and they can proactively set limits to manage costs. With the addition of AWS Lambda, compute is faster, and researchers can keep their costs down by only paying to store and compute while the pipeline is running data in Amazon Elastic Compute Cloud (Amazon EC2).

Explore more on this in the post, ‘Tracking global antimicrobial resistance among pathogens using Nextflow and AWS’ and learn how the CGPS and collaborating labs are using this solution to take their research and public health reporting to a degree of specificity that was not possible with traditional microbiology.

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Kelli Jonakin, Ph.D.

Kelli Jonakin, Ph.D.

Kelli Jonakin is the Principal Marketing Manager for the Life Sciences and Genomics Industry verticals at AWS. She comes with a background in pharmaceutical research, with a special focus on development and commercialization of biologics. Kelli received her Ph.D. in Pharmacology and Systems Biology from the University of Colorado, and received an NIH post-doctoral fellowship grant to study Biochemistry at the University of Wisconsin-Madison.