pasty
Tags: pseudomonas-aeruginosa serogroup typing o-antigen prediction sample-scope
Predict serogroups of Pseudomonas aeruginosa from assemblies.
This subworkflow uses Pasty to perform in silico serogrouping of Pseudomonas aeruginosa isolates from assembled genomes. It identifies O-antigen biosynthesis genes to classify isolates into their known serogroups using BLAST-based homology searches.
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 O-antigen serogroup |
blast | A tab-delimited file of all raw BLAST hits used for the prediction |
details | A tab-delimited file with detailed gene hits for each serogroup tested |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- pasty - Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- pasty - In silico serogrouping of Pseudomonas aeruginosa isolates.
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) -
pasty
Petit III RA pasty: in silico serogrouping of Pseudomonas aeruginosa isolates (GitHub)