GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.

ABSTRACT: Streptococcus pneumoniae (pneumococcus) is a major pathogen globally, responsible for an estimated one million deaths annually and contributing significantly to the global burden of antimicrobial resistance. Ongoing surveillance of its vaccine antigen (i.e. serotypes), antimicrobial resistance, and pneumococcal lineages is crucial for assessing the impact of vaccination programs and guiding future vaccine design. However, current bioinformatics tools have several limitations that prevent them from enabling comprehensive analysis that allows simultaneous, large-scale, and independent generation of these crucial data. Here, we present the GPS Pipeline that enables reliable extraction of public health information from pneumococcal genomes using in silico methods. It can accurately identify 10

SUBMITTER: Hung HCH 

PROVIDER: S-EPMC12460886 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature