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
For full workflow details check Workflow documentation
Nextflow(>=22.10.1)- One container runtime:
Docker(recommended for local runs)Apptainer(recommended for HPC)Singularity
Prepare a samplesheet (CSV) to define sample files and organisms:
sample,fastq_1,fastq_2,assembly,organism
SAMPLE_1,/path/S1_R1.fastq.gz,/path/S1_R2.fastq.gz,/path/S1.fasta,Escherichia_coli
SAMPLE_2,/path/S2_R1.fastq.gz,/path/S2_R2.fastq.gz,/path/S2.fasta,Salmonella
SAMPLE_3,/path/S3.fastq.gz,,/path/S3.fasta,Shigella
SAMPLE_4,,,/path/S4.fasta,Pseudomonas_aeruginosa
SAMPLE_5,/path/S5_R1.fastq.gz,/path/S5_R2.fastq.gz,/path/S5.fasta,Legionella_pneumophila
Input format description
| Column | Description |
|---|---|
sample |
Unique sample ID |
fastq_1 |
Path to trimmed read 1 (leave empty if not available) |
fastq_2 |
Path to trimmed read 2 (leave empty for single-end, ONT or assemblies) |
assembly |
FASTA assembly |
organism |
Supported organism name (can be Other if running ABRicate for any other species) |
Important
- Most analyses require assemblies as input. However, tools such as
el_gatoandSeqSero2may provide more accurate results when reads are supplied. - Reads are required for
ShigaTyper,SeroBA, andARIBA. If reads are not provided for a sample, these analyses will be skipped for that sample.
Note
If the reads are from ONT, add the flag --ont when running your analyses. ONT reads are only supported for ECTyper, SeqSero2, and ShigaTyper
Supported inputs per tool
| Organism | Tool | Aim | fastq1 | fastq2 | Assembly |
|---|---|---|---|---|---|
| Acinetobacter baumannii | Kaptive with Wyres et. al database |
Serotyping based on K and OC antigens | - | - | ✔️ |
| Escherichia coli | ECTyper |
Serotyping based on O/H antigens; optional pathotyping (only when using --ecoli_pathotypes) |
Fallback |
- | Preferred ✔️ |
| Haemophilus influenzae | HICap |
Serotyping based on cap locus (a–f) | - | - | ✔️ |
| Klebsiella pneumoniae complex | Kleborate |
Serotyping (K/O), MLST, virulence genes | - | - | ✔️ |
| Legionella pneumophila | el_gato |
Sequence‑based typing (SBT) | Preferred ✔️ | Preferred ✔️ | Fallback |
| Legionella pneumophila | ABRicate with ReporType databases |
O‑antigen serogrouping (wzm/wzt) and subsepcies | - | - | ✔️ |
| Listeria monocytogenes | LisSero |
Serogrouping/serotyping (O/H) | - | - | ✔️ |
| Neisseria gonorrhoeae | NGMASTER |
porB/tbpB typing; AMR typing | - | - | ✔️ |
| Neisseria meningitidis | meningotype |
Serogrouping (capsule); MLST; BAST; MenDeVAR | - | - | ✔️ |
| Pseudomonas aeruginosa | Pasty |
Serotyping based on O antigen | - | - | ✔️ |
| Salmonella | SeqSero2 |
Serotyping and antigenic profile | Preferred ✔️ (can be ONT) | Preferred ✔️ (optional for single-end or ONT) | Fallback |
| Salmonella | SISTR |
Serovar prediction via antigen genes + cgMLST | - | - | ✔️ |
| Shigella | ShigaTyper |
Serotyping + ipaB | ✔️ (can be ONT) | ✔️ (optional for single-end or ONT) | - |
| Shigella | ShigEiFinder |
Shigella/EIEC diff.; serotyping; virulence plasmid | Fallback |
Fallback |
Preferred ✔️ |
| Staphylococcus aureus | AgrVATE |
agr locus typing | - | - | ✔️ |
| Staphylococcus aureus | sccmec |
SCCmec cassette typing | - | - | ✔️ |
| Staphylococcus aureus | spaTyper |
spa repeat typing | - | - | ✔️ |
| Streptococcus dysgalactiae | emmtyper |
emm type assignment | - | - | ✔️ |
| Streptococcus pneumoniae | pbptyper |
PBP typing | - | - | ✔️ |
| Streptococcus pneumoniae | SeroBA |
Serotyping via cps locus | ✔️ | ✔️ | - |
| Streptococcus pyogenes | emmtyper |
emm type assignment | - | - | ✔️ |
| Vibrio parahaemolyticus | Kaptive with Zomer Lab databases |
K/O serotyping | - | - | ✔️ |
| Vibrio cholerae | ARIBA |
Detect ctxA, ctxB, tcpA, rstR | ✔️ | ✔️ | - |
| Vibrio cholerae | Kaptive with VicPred OAGC database |
O‑antigen serotyping | - | - | ✔️ |
| Other (and any supported organism) | ABRicate |
Locus detection, any db via --abricate_db |
- | - | ✔️ |
ABRicate bundles multiple databases for the detection of resistance determinants and virulence factors. This tool is optional and available for any organism in the sample sheet when using --abricate_db <database>. Only one database can be used per run:
| Database | Description | Gene Types |
|---|---|---|
| argannot | Antibiotic resistance gene annotation | AMR genes |
| bacmet2 | Bacterial biocide & metal resistance genes | Metal/biocide resistance |
| card | Comprehensive Antibiotic Resistance Database | AMR genes |
| ecoh | E. coli virulence genes (subset) | Virulence factors |
| ecoli_vf | Expanded E. coli virulence gene set | Virulence factors |
| megares | Antibiotic resistance ontology | AMR genes |
| ncbi | NCBI AMRFinder+ gene set | AMR genes |
| plasmidfinder | Plasmid replicon typing | Plasmid replicons |
| resfinder | Resistance gene detection | AMR genes |
| upec_expec_vf | UPEC/ExPEC virulence markers | Virulence factors |
| vfdb | Virulence Factor Database | Virulence genes |
| victors | Bacterial virulence database | Virulence genes |
Now, you can run the pipeline using:
nextflow run MDHHS-Bioinformatics/basset \
-profile apptainer \
--input samplesheet.csv \
--outdir basset_resultsFor advance run including species-specific analyses and ABRicate:
nextflow run MDHHS-Bioinformatics/basset \
-profile apptainer \
--input samplesheet.csv \
--outdir basset_results \
--abricate_db vfdb \
--ecoli_pathotypes \
--max_memory 50.GB \
--max_cpus 8 \
--max_time 4.hFor more details and further functionality, please refer to Usage documentation and the Parameter documentation
Results are organized by organism except by the ABRicate results:
📁 <outdir>/
├── 📁 <Organism>/
| └── 📄<sample>_<tool>_<out_name>.tsv
| └── 📄<sample>_<tool>_summary.tsv
├── 📁 abricate/ (only if --abricate_db <database>)
| └── 📄<sample>_abricate_<db>.tsv
├── 📄basset_summary_batch.tsv
└── 📄basset_summary_master.tsv
Key outputs:
- BaSSeT summary batch
- BaSSeT summary master
For more details about the output files and reports, please refer to the Output documentation
BaSSeT was built and is maintained by the Genomic Analysis Unit at the Michigan Department of Health & Human Services (MDHHS) Bureau of Laboratories. This pipeline was developed by Karla Vasco using the nf-core template.
Additional conceptual guidance and scientific input were provided by Arianna Miles-Jay and Heather Blankenship.
Contributions, issues, and pull requests are welcome! If you would like to contribute to this pipeline, please see the Contribution guidelines.
If you use BaSSeT for your analysis, please cite the following doi:
Vasco K., Blankenship H. & Miles-Jay A. (2026). MDHHS-Bioinformatics/basset: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.20856443
An extensive list of references for the tools used by the pipeline can be found in CITATIONS.md.
This repository is not a source of government records but is intended to increase collaboration and collaborative potential on public health related projects. Materials and information in this repository are intended to share information and collaboratively develop analysis workflows.
The workflows and pipelines reflect the current understanding of the software and biological questions being answered and may be updated as needed and pursuant to further analysis and review. No warranty, expressed or implied, is made by MDHHS Bureau of Laboratories as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that the MDHHS Bureau of Laboratories shall not be held liable for any damages resulting from its authorized or unauthorized use.
Use of this service is limited only to non-sensitive and publicly available data. Users must not use, share, or store any kind of sensitive data like health status, provision or payment of healthcare, Personally Identifiable Information (PII) and/or Protected Health Information (PHI), etc. under any circumstance.
This project is released under the MIT License.