pbptyper

Tags: bacteria streptococcus-pneumoniae penicillin amr resistance pbp typing sample-scope

Predict Penicillin Binding Protein (PBP) type of Streptococcus pneumoniae assemblies.

Uses PBPtyper to detect variations in the three key PBP genes (pbp1a, pbp2b, and pbp2x) in S. pneumoniae. Typing these genes is essential for predicting reduced susceptibility or full resistance to penicillin and other $\beta$-lactam antibiotics.

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,
    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 PBP type for each gene
blast	Path	A tab-delimited file of the raw TBLASTN hits used for gene identification
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

pbptyper Parameters

Parameter	Type	Default	Description
--pbptyper_min_pident	integer	95	Minimum percent identity to count a hit
--pbptyper_min_coverage	integer	95	Minimum percent coverage to count a hit

Used By

Subworkflows

• pbptyper - Predict penicillin binding protein (PBP) types of Streptococcus pneumoniae from genome assemblies.

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)

Source

View source on GitHub

Version

PBPTYPER:
    - pbptyper: 2.0.0