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Outputs
This document describes the outputs generated by BaSSeT.
All paths described below are relative to the pipeline output directory specified with:
--outdir
Results are organized by organism except by the ABRicate results:
📁 <outdir>
├── 📁 abricate (only if --abricate_db <database>)
│ └── 📄 <sample>_abricate_<database>.tsv
├── 📁 Acinetobacter_baumannii
│ ├── 📄 <sample>_kaptive_k.tsv
│ ├── 📄 <sample>_kaptive_oc.tsv
│ └── 📄 <sample>_kaptive_summary.tsv
├── basset_summary_batch.tsv
├── basset_summary_master.tsv
├── 📁 Escherichia_coli
│ ├── 📄 <sample>_ectyper_blastn_output_alleles.txt
│ ├── 📄 <sample>_ectyper.log
│ ├── 📄 <sample>_ectyper_output.tsv
│ └── 📄 <sample>_ectyper_summary.tsv
├── 📁 Haemophilus_influenzae
│ ├── 📄 <sample>_hicap.gbk
│ ├── 📄 <sample>_hicap_output.tsv
│ ├── 📄 <sample>_hicap_summary.tsv
│ └── 📄 <sample>_hicap.svg
├── 📁 Klebsiella_pneumoniae_complex
│ ├── 📄 <sample>_kleborate_output.tsv
│ └── 📄 <sample>_kleborate_summary.tsv
├── 📁 Legionella_pneumophila
│ ├── 📄 <sample>_abricate_lp_serogroup.tsv
│ ├── 📄 <sample>_abricate_lp_subspecies.tsv
│ ├── 📄 <sample>_abricate_lp_summary.tsv
│ ├── 📄 <sample>_elgato_intermediate_outputs.txt
│ ├── 📄 <sample>_elgato_possible_mlsts.txt
│ ├── 📄 <sample>_elgato_report.json
│ ├── 📄 <sample>_elgato_run.log
│ └── 📄 <sample>_el_gato_summary.tsv
├── 📁 Listeria_monocytogenes
│ ├── 📄 <sample>_lissero_output.tsv
│ └── 📄 <sample>_lissero_summary.tsv
├── 📁 Neisseria_gonorrhoeae
│ ├── 📄 <sample>_ngmaster_output.tsv
│ └── 📄 <sample>_ngmaster_summary.tsv
├── 📁 Neisseria_meningitidis
│ ├── 📄 <sample>_meningotype_output.tsv
│ └── 📄 <sample>_meningotype_summary.tsv
├── 📁 pipeline_info
│ ├── 📄 execution_report_YYYY-MM-DD_HH-MM-SS.html
│ ├── 📄 execution_timeline_YYYY-MM-DD_HH-MM-SS.html
│ ├── 📄 execution_trace_YYYY-MM-DD_HH-MM-SS.txt
│ ├── 📄 pipeline_dag_YYYY-MM-DD_HH-MM-SS.html
│ ├── 📄 samplesheet.valid.csv
│ └── 📄 software_versions.yml
├── 📁 Pseudomonas_aeruginosa
│ ├── 📄 <sample>_pasty.blastn.tsv
│ ├── 📄 <sample>_pasty.details.tsv
│ ├── 📄 <sample>_pasty_output.tsv
│ └── 📄 <sample>_pasty_summary.tsv
├── 📁 Salmonella
│ ├── 📄 <sample>_seqsero2_summary.tsv
│ ├── 📄 <sample>_SeqSero_log.txt
│ ├── 📄 <sample>_SeqSero_result.tsv
│ ├── 📄 <sample>_SeqSero_result.txt
│ ├── 📄 <sample>_sistr_output.csv
│ └── 📄 <sample>_sistr_summary.tsv
├── 📁 Shigella
│ ├── 📄 <sample>_shigatyper_hits.tsv
│ ├── 📄 <sample>_shigatyper_output.tsv
│ ├── 📄 <sample>_shigatyper_summary.tsv
│ ├── 📄 <sample>_shigeifinder_output.tsv
│ └── 📄 <sample>_shigeifinder_summary.tsv
├── 📁 Staphylococcus_aureus
│ ├── 📄 <sample>_agrvate_agr_gp.tab
│ ├── 📄 <sample>_agrvate_output.tsv
│ ├── 📄 <sample>_agrvate_summary.tsv
│ ├── 📄 <sample>_sccmec_output.tsv
│ ├── 📄 <sample>_sccmec.regions.blastn.tsv
│ ├── 📄 <sample>_sccmec.regions.details.tsv
│ ├── 📄 <sample>_sccmec_summary.tsv
│ ├── 📄 <sample>_sccmec.targets.blastn.tsv
│ ├── 📄 <sample>_sccmec.targets.details.tsv
│ ├── 📄 <sample>_spatyper_output.tsv
│ └── 📄 <sample>_spatyper_summary.tsv
├── 📁 Streptococcus_pneumoniae
│ ├── 📄 <sample>_pbptyper_output.tsv
│ ├── 📄 <sample>_pbptyper_summary.tsv
│ ├── 📄 <sample>_pbptyper_tblastn.tsv
│ ├── 📄 <sample>_seroba_output.csv
│ └── 📄 <sample>_seroba_summary.tsv
├── 📁 Streptococcus_pyogenes
│ ├── 📄 <sample>_emmtyper_summary.tsv
│ └── 📄 <sample>_emmtyper.tsv
├── 📁 Vibrio_cholerae
│ ├── 📄 <sample>_ariba_output.tsv
│ ├── 📄 <sample>_ariba_summary.tsv
│ ├── 📄 <sample>_kaptive_o.tsv
│ └── 📄 <sample>_kaptive_summary.tsv
└── 📁 Vibrio_parahaemolyticus
├── 📄 <sample>_kaptive_k.tsv
├── 📄 <sample>_kaptive_o.tsv
└── 📄 <sample>_kaptive_summary.tsv
BaSSeT outputs summaries per batch basset_summary_batch.tsv and appends new typing results to a master file basset_summary_master.tsv
File:
basset_summary_batch.tsv
basset_summary_master.tsv
These files concatenate results from different typing tools and organisms into a single file.
Results from ABRicate or E. coli pathotypes are not included in the summary.
| Column | Description |
|---|---|
sample |
Sample identifier |
organism |
Supported organism |
tool |
Tool name |
result_type |
Analysis or antigenic marker |
result_value |
Typing result |
tool_version |
Tool version used in the analysis |
basset_version |
BaSSeT version used in the analysis |
analysis_date |
YYYY-MM-DD |
Detailed tool outputs are stored in the corresponding organism subdirectories.
ABRicate is used for mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB, VICTORS, BacMet, UPEC/ExPEC VF
Files
| File | Description |
|---|---|
<sample>_abricate_<database>.tsv |
ABRicate results |
Kaptive is used for surface polysaccharide typing from bacterial genome sequences, including: Klebsiella pneumoniae complex (K and O), Acinetobacter baumanni (K and OC), Vibrio cholerae (O) and Vibrio parahaemolitycus (O).
Note
- BaSSeT summaries report Vibrio cholerae serotype predictions only at the major group level: O1, O139, non-O1/non-O139, or unassigned (-). This reporting approach is based on concordance evaluation between Kaptive and VicPred, which showed complete agreement (100%) for major serogroup classification but lower agreement for O1 variant (80%) and non-O1/non-O139 serotype-level (63%) comparisons.
- For more detailed typing results, users should inspect the full Kaptive output. Assignment of O1-Inaba or O1-Ogawa should be interpreted with caution and further investigated based on the status of the wbeT gene.
Files
| File | Description |
|---|---|
<sample>_kaptive_k.tsv |
K locus typing |
<sample>_kaptive_o.tsv |
O locus typing |
<sample>_kaptive_oc.tsv |
OC locus typing |
<sample>_kaptive_summary.tsv |
BaSSet-formated results |
ECTyper is used for Escherichia coli characterization including species identification, in silico serotyping covering O and H antigens, Shiga toxin typing and DEC pathotyping.
Files
| File | Description |
|---|---|
<sample>_ectyper_blastn_output_alleles.txt |
Hits of the O and H antigen database |
<sample>_ectyper_output.tsv |
Main report |
<sample>_ectyper_summary.tsv |
BaSSet-formated results |
<sample>_ectyper.log |
Log messages |
HICap is used for serotyping of Haemophilus influenzae based on cap locus (a–f)
Files
| File | Description |
|---|---|
<sample>_hicap_output.tsv |
detailed summary information |
<sample>_hicap_summary.tsv |
BaSSet-formated results |
<sample>_hicap.gbk |
genbank file with sequence marked up with cap locus annotations |
<sample>_hicap.svg |
visual representation of the annotated cap locus |
Kleborate is primarily developed to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:
- Species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
- K. pneumoniae species complex MLST
- ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmp)
- Virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmp, rmpA2)
- Antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
- Prediction of phenotypic resistance to ciprofloxacin
- K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive
Files
| File | Description |
|---|---|
<sample>_kleborate_output.tsv |
Klebsiella typing results |
<sample>_kleborate_summary.tsv |
BaSSet-formated results |
el_gato is used to output Legionella pneumophila Sequence Type (ST).
Files
| File | Description |
|---|---|
<sample>_elgato_summary.tsv |
BaSSet-formated results |
<sample>_elgato_intermediate_outputs.txt |
Log messages of intermediate analyses |
<sample>_elgato_possible_mlsts.txt |
All possible ST profiles in case multiple possible alleles are identified for any ST loci |
<sample>_elgato_repot.json |
Results as JSON file which can be used to generate a PDF report |
<sample>_elgato_run.log |
Detailed log |
ABRicate is used to identify the best-matching subspecies and wzm/wzt alleles for O-antigen serogrouping of Legionella pneumophila. Internal evaluation showed an accuracy of 99.26% for serogroup 1, but only 15.63% for the other evaluated serogroups. Therefore, serogroup prediction is currently supported only for serogroup 1. For all other serogroups, the workflow reports the best matches for each gene marker without assigning a supported serogroup prediction. The databases used for this analysis were obtained from ReporType.
Files
| File | Description |
|---|---|
<sample>_abricate_lp_summary.tsv |
BaSSet-formated results |
<sample>_abricate_lp_serogroup.tsv |
ABRicate results for wzm/wzt alleles |
<sample>_abricate_lp_subspecies.tsv |
ABRicate results for Legionella pneumophila subsepecies |
LisSero is used for Listeria monocytogenes serogrouping/serotyping (O/H)
Files
| File | Description |
|---|---|
<sample>_lissero_summary.tsv |
BaSSet-formated results |
<sample>_lissero_output.txt |
LisSero output |
NGMASTER is used for Neisseria gonorrhoeae porB/tbpB typing; AMR typing
Files
| File | Description |
|---|---|
<sample>_ngmaster_summary.tsv |
BaSSet-formated results |
<sample>_ngmaster_output.txt |
NGMASTER output |
meningotype is used for Neisseria meningitidis serogrouping (capsule); MLST; BAST; MenDeVAR
Files
| File | Description |
|---|---|
<sample>_meningotype_summary.tsv |
BaSSet-formated results |
<sample>_meningotype_output.txt |
meningotype output |
Pasty is used for Pseudomonas aeruginosa serotyping based on O antigen
Files
| File | Description |
|---|---|
<sample>_pasty_summary.tsv |
BaSSet-formated results |
<sample>_pasty_output.txt |
Pasty output with the predicted serogroup |
<sample>_pasty.blastn.tsv |
A tab-delimited file of all blast hits |
<sample>_pasty.details.tsv |
A tab-delimited file with details for each serogroup |
SeqSero2 is used for Salmonella serotyping and antigenic profiling
Files
| File | Description |
|---|---|
<sample>_seqsero2_summary.tsv |
BaSSet-formated results |
<sample>_SeqSero_log.txt |
Blast results |
<sample>_SeqSero_result.tsv |
SeqSero results as tab-delimited file |
<sample>_SeqSero_result.txt |
SeqSero results as txt file |
SISTR is used for Salmonella serovar prediction via antigen genes + cgMLST
Files
| File | Description |
|---|---|
<sample>_sistr_summary.tsv |
BaSSet-formated results |
<sample>_sistr_output.csv |
SISTR results |
ShigaTyper is used for Shigella serotyping + ipaB
Files
| File | Description |
|---|---|
<sample>_shigatyper_summary.tsv |
BaSSet-formated results |
<sample>_shigatyper_output.tsv |
ShigaTyper results |
<sample>_shigatyper_hits.tsv |
Statistics about each individual gene hit |
ShigEiFinder is a tool for differentiating Shigella/EIEC using cluster-specific genes and identifying the serotype using O-antigen/H-antigen genes.
Files
| File | Description |
|---|---|
<sample>_shigeifinder_summary.tsv |
BaSSet-formated results |
<sample>_shigeifinder_output.tsv |
ShigEiFinder results |
AgrVATE is a tool for rapid identification of Staphylococcus aureus agr locus type and also reports possible variants in the agr operon.
Files
| File | Description |
|---|---|
<sample>_agravate_summary.tsv |
BaSSet-formated results |
<sample>_agravate_output.tsv |
AgrVATE results |
<sample>_agravate_agr_gp.tab |
AgrVATE blast results |
sccmec is a tool for typing SCCmec cassettes in Staphylococcus aureus assemblies
Files
| File | Description |
|---|---|
<sample>_sccmec_summary.tsv |
BaSSet-formated results |
<sample>_sccmec_output.tsv |
sccmec results with the predicted type |
<sample>_sccmec.regions.blastn.tsv |
A tab-delimited file of all full cassette blast hits |
<sample>_sccmec.regions.details.tsv |
A tab-delimited file with details for each type based on targets |
<sample>_sccmec.targets.blastn.tsv |
A tab-delimited file of all target-specific blast hitss |
<sample>_sccmec.targets.details.tsv |
A tab-delimited file with details for each type based on targets |
spaTyper is a tool for Staphylococcus aureus spa repeat typing
Files
| File | Description |
|---|---|
<sample>_spatyper_summary.tsv |
BaSSet-formated results |
<sample>_spatyper_output.tsv |
spaTyper results with the predicted type |
pbptyper is a tool for in silico Penicillin Binding Protein (PBP) typing of Streptococcus pneumoniae
Files
| File | Description |
|---|---|
<sample>_pbptyper_summary.tsv |
BaSSet-formated results |
<sample>_pbptyper_output.tsv |
pbptyper results with the predicted type |
<sample>_pbptyper_tblastn.tsv |
blast hits |
SeroBA is a k-mer based Pipeline to identify the Serotype of Streptococcus pneumoniae from Illumina NGS reads for given references
Files
| File | Description |
|---|---|
<sample>_seroba_summary.tsv |
BaSSet-formated results |
<sample>_seroba_output.csv |
seroba results with the predicted type |
emmtyper is tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly.
Files
| File | Description |
|---|---|
<sample>_emmtyper_summary.tsv |
BaSSet-formated results |
<sample>_emmtyper_output.tsv |
emmtyper results with the predicted type |
ARIBA is a tool used to identify the Vibrio cholerae virulence genes ctxA, ctxB, tcpA, rstR by running local assemblies.
Files
| File | Description |
|---|---|
<sample>_ariba_summary.tsv |
BaSSet-formated results |
<sample>_ariba_output.tsv |
ARIBA results for the detected virulence genes |
Directory:
pipeline_info/
This directory contains Nextflow execution reports.
Files
| File | Description |
|---|---|
execution_report.html |
Pipeline execution summary |
execution_timeline.html |
Task timeline |
execution_trace.txt |
Detailed resource usage |
pipeline_dag.svg |
Workflow graph |
software_versions.yml |
Software versions used |
These files are useful for reproducibility and troubleshooting.