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.
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