SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

ABSTRACT: Streptococcus pneumoniae is responsible for 240 000-460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can pre

SUBMITTER: Epping L 

PROVIDER: S-EPMC6113868 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature