pbptyper
Tags: streptococcus-pneumoniae pbp-typing penicillin antimicrobial-resistance sample-scope
Predict penicillin binding protein (PBP) types of Streptococcus pneumoniae from genome assemblies.
This subworkflow uses pbptyper to predict the penicillin binding protein (PBP) types and predict antimicrobial susceptibility of Streptococcus pneumoniae strains from assembled genomes. It processes each sample individually and aggregates the results into a single consolidated report.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | A tab-delimited summary file with the predicted PBP type for each gene |
blast | A tab-delimited file of the raw TBLASTN hits used for gene identification |
details | Detailed PBP typing results for each gene analyzed |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- pbptyper - Predict Penicillin Binding Protein (PBP) type of Streptococcus pneumoniae assemblies.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- pbptyper - Penicillin Binding Protein (PBP) typing for Streptococcus pneumoniae.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
pbptyper
Petit III RA pbptyper: In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies (GitHub)