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BaSSeT (Bacterial Species-Specific Typing) is a bioinformatics pipeline for species-specific typing of bacteria. It takes a samplesheet with reads (FASTQ) and assembly (FASTA) files of multiple isolates from different organisms; performs species-specific typing analysis, produces a summary report per batch and combines new and prior results into a master results file.
BaSSeT is designed to analyze QC-trimmed reads and genome assemblies generated by sequencing pipelines such as PHoeNIx, Bactopia, TheiaProk, custom workflows, or retrieved from public databases such as AllTheBacteria and NCBI. The pipeline provides species-specific predictions for serotyping or serogrouping, virulence gene detection, and other analyses that complement higher-resolution typing approaches such as MLST and cgMLST. These outputs can support epidemiological investigations and genomic population analyses.
BaSSeT is not intended to be an end-to-end read QC or assembly pipeline. Instead, it is designed to avoid duplicating upstream quality-control steps while providing a portable and reproducible framework for typing diverse bacterial organisms.
- 🦠 Processes multiple organisms in parallel
- 🧬 Supports 24 different typing analyses
- 📄 Generates summary results with tool versions per batch
- 📄 New and prior results are appended to a master file
High-level steps:
- Input check
- ABRicate if
--abricate_db <database>specified - Species specific analyses
- Batch summary generation
- Master summary generation