phispy

Tags: genomics virus phage prophage bacteriophage identification annotation sample-scope

Predict prophage regions integrated into bacterial genomes.

Uses PhiSpy to identify integrated bacteriophage (prophage) regions in a fully annotated bacterial genome. The prediction relies on scoring features like strand-switch, AT-skew, unique phage-like proteins, and short coding regions.

Inputs

record (
    meta: Record,
    gbff: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
gbff	Path	Annotated genome file in GenBank format

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Coordinates (start/end) of each predicted prophage region in the genome
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

PhiSpy Parameters

Parameter	Type	Default	Description
--phispy_number	integer	5	Number of consecutive genes in a region of window size that must be prophage genes to be called
--phispy_mincontigsize	integer	5000	Minimum contig size (in bp) to be included in the analysis. Smaller contigs will be dropped.
--phispy_opts	string		Extra options in quotes for PhiSpy

Used By

Subworkflows

• phispy - Prediction of prophages from bacterial genomes.

Workflows

• phispy - Prediction of prophages in bacterial and archaeal genomes.

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)

• PhiSpy
  Akhter S, Aziz RK, and Edwards RA PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Research, 40(16), e126. (2012)

Source

View source on GitHub

Version

PHISPY:
    - phispy: 5.0.6