phispy
Tags: prophage phage bacterial genome mobile-genetic-elements sample-scope
Prediction of prophages from bacterial genomes.
This subworkflow identifies prophages in bacterial genomes using PhiSpy, which combines similarity-based and composition-based strategies for accurate detection. The tool identifies integrated phage sequences, extracts bacterial and phage regions, and provides comprehensive annotation including GFF format for downstream analysis.
Take
gbff: Channel<Record>
| Name | Description |
|---|---|
gbff | Annotated bacterial genomes in GenBank format for prophage prediction |
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 | Coordinates (start/end) of each predicted prophage region in the genome |
supplemental | Directory containing detailed prophage information, sequences, and annotations |
run_outputs
| Output | Description |
|---|---|
csv | Merged prophage prediction results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- phispy - Predict prophage regions integrated into bacterial genomes.
Used By
This subworkflow is used by the following 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)