Version 3: RSYD-BASIC: a bioinformatics pipeline for Routine Sequence analYsis and Data processing of BActerial iSolates for clInical miCrobiology

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

 When tested on publicly available sequences, our pipeline yields comparable results in most cases. In routine use, it has already yielded clinically relevant results, allowing us to type a variety of bacterial pathogens isolated in our clinical laboratory and disprove a potential outbreak.

Conclusion

With the RSYD-BASIC pipeline, we present a reads-to-results analysis pipeline operated by non-expert users that greatly eases investigation of potential outbreaks. Results obtained with publicly available sequences are also promising, while underlining the importance of standardized methods.