Scalable Pathogen Pipeline Platform (SP^3): Enabling Unified Genomic Data Analysis with Elastic Cloud Computing


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.



Software And Hardware

• Hardware: Processor: i3 ,i5 RAM: 4GB Hard disk: 16 GB • Software: operating System : Windws2000/XP/7/8/10 Anaconda,jupyter,spyder,flask Frontend :-python Backend:- MYSQL