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Scalable pathogen pipeline platform (SP^3): enabling unified genomic data analysis with elastic cloud computing

Yang-Turner, Fan, Volk, Denis, Fowler, Philip, Swann, Jeremy, Bull, Matthew, Hoosdally, Sarah, Connor, Thomas, Peto, Tim and Crook, Derrick 2019. Scalable pathogen pipeline platform (SP^3): enabling unified genomic data analysis with elastic cloud computing. Presented at: IEEE 12th International Conference on Cloud Computing (CLOUD), Milan, Italy, 8-13 Jul 2019. Proceedings of IEEE 12th International Conference on Cloud Computing (CLOUD). IEEE, pp. 478-480. 10.1109/CLOUD.2019.00083

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Abstract

Pathogen genomic data analysis can be extremely bespoke and diverse. This paper presents our plan and progress towards creating a Scalable Pathogen Pipeline Platform (SP 3 ) providing an efficient and unified process of collecting, analysing and comparing genomic data analysis with the benefit of elastic cloud computing. SP 3 enables container-centric bioinformatic workflows run on personal computers, High-performance computing (HPC) clusters and cloud platforms. We have deployed and tested SP 3 on local HPC, Google Cloud Platform (GCP), Microsoft Azure and OpenStack Platforms. SP 3 allows users to fetch genomic sequencing data from European Nucleotide Archive (ENA) and conduct analysis with open-source bioinformatic pipelines. We believe SP 3 will promote common standards around pathogen genomic data quality, data processing and data analysis, helping answer the challenges of tools divergence and leveraging a pool of public genomic data repository and cloud resources.

Item Type: Conference or Workshop Item (Paper)
Date Type: Published Online
Status: Published
Schools: Biosciences
Publisher: IEEE
Last Modified: 31 Jan 2020 03:36
URI: http://orca-mwe.cf.ac.uk/id/eprint/125841

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