pasty

Tags: bacteria pseudomonas-aeruginosa serogroup o-antigen typing blast sample-scope

Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.

Uses Pasty (in silico serogrouping of Pseudomonas aeruginosa isolates) to predict the O-antigen serogroup by searching the genome assembly for specific serogroup-associated genes within the O-antigen locus.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    blast: Path,
    details: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	A tab-delimited summary file with the predicted O-antigen serogroup
blast	Path	A tab-delimited file of all raw BLAST hits used for the prediction
details	Path	A tab-delimited file with detailed gene hits for each serogroup tested
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

pasty Parameters

Parameter	Type	Default	Description
--pasty_min_pident	integer	95	Minimum percent identity to count a hit
--pasty_min_coverage	integer	95	Minimum percent coverage to count a hit

Used By

Subworkflows

• pasty - Predict serogroups of Pseudomonas aeruginosa from assemblies.

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)

Source

View source on GitHub

Version

PASTY:
    - pasty: 2.2.1