SP3: Scalable Software for Pathogen Reads to Clinical Results using Next Generation Sequencing (360G-Wellcome-215800_Z_19_Z)

Scalable Pathogen Pipeline for turning Next Generation Sequencing Pathogen data into Clinical Results Recently, technology has developed which allows us to read the DNA blueprint of microbes rapidly. This technology is now being widely used on bacteria, both to decide optimal treatments, and to track the transmission of infection. A key requirement is the need for integrated software to turn DNA sequence data into a microbial identification and a prediction of resistance, and into a usable depiction of microbial transmission. Existing software solutions work and improve on conventional laboratory methods, but are difficult to deploy and validate outside the University settings where they were created. However, there is global demand for similar, readily deployed, high quality services. The Scalable Pathogen Pipeline (SP3) project will address this demand. Building on a range of proven existing tools, it will provide a sustainable, open source, software framework, together with validation data, to clinical and research settings. It will be deployable without the need for extensive software or genomics expertise.