Hung, H. C. H.; Kumar, N.; Dyster, V.; Yeats, C.; Metcalf, B.; Li, Y.; Hawkins, P. A.; McGee, L.; Bentley, S. D.; Lo, S. W.

Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-friendly tools to effectively analyse the increasing volume of data. To meet this need, we have developed a genomic analysis pipeline, GPS Pipeline, which is portable and scalable to analyse genomes of Streptococcus pneumoniae, a major bacterial pathogen that is estimated to cause 317,000 child deaths worldwide every year. The GPS Pipeline is based on Nextflow and containerisation technology, and designed to enable researchers generating public health relevant output, including in silico serotypes, pneumococcal lineages (i.e. GPSCs), multilocus sequence types, and antimicrobial susceptibilities against 20 commonly used antibiotics, with minimal software setup requirements and bioinformatic expertise, in order to analyse genomic data at scale with ease. The GPS Pipeline provides a streamlined workflow that improves responsiveness in genomic surveillance on pneumococci.