RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for clinical microbiology.

ABSTRACT: Background. Whole-genome sequencing of bacterial isolates is increasingly becoming routine in clinical microbiology; however, subsequent analysis often needs to be started by a bioinformatician even for comprehensive pipelines. To increase the robustness of our workflow and free up bioinformatician work hours for development and advanced analysis, we aimed to produce a robust, customizable bioinformatic pipeline for bacterial genome assembly and routine analysis results that could be initiated by non-bioinformaticians. Results. We introduce the RSYD-BASIC pipeline for bacterial isolate sequence analysis and provide a demonstration of its functionality with two datasets composed of publicly available sequences, in which comparable results are obtained in most cases. In some in

SUBMITTER: Steinke K 

PROVIDER: S-EPMC11927588 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature