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

We want to allow the benefits of pathogen genomics to be realised widely, without the need for extensive local software development or genomics expertise. In human genetics there are standards around how variants are called, implemented in well documented, accessible software solutions permitting results generated in one laboratory to be comparable to those generated elsewhere. We wish to see the same thing for pathogen genomics, and believe that stumbling blocks have been lack of (i) highly documented, modular and comprehensive analysis frameworks (SP3), (ii) transfer of knowledge from those who have deployed approaches successfully to early adopters, and (iii) sharing of well characterised data sets suitable for clinical validation. The funding requested will allow us to complete these goals. Crucially, while the documentation, data, and SP3 software provided will provide fully functional components for key microbes, our work will also provide a framework both for analysis of new organisms with existing tools, and for the introduction of new components addressing emerging objectives. The release of these resources, together with the engagement of multiple publically funded bodies involved in diagnostics and Health Protection, will yield a broadly supported, durable open source project providing core functions for pathogen genomics and public health.