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.