phispy

Tags: prophage phage annotation bacterial archaeal bactopia-tool

Prediction of prophages in bacterial and archaeal genomes.

This Bactopia Tool uses PhiSpy to identify prophages from bacterial and archaeal genomes using machine learning approaches.

Usage

Bactopia CLI:

bactopia --wf phispy \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/phispy/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── phispy-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.tsv
│           ├── logs
│           │   ├── <SAMPLE_NAME>.log
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               └── <SAMPLE_NAME>_<SAMPLE_NAME>.gbk.gz
├── GCF_900478275
│   └── tools
│       └── phispy-<TIMESTAMP>
│           ├── GCF_900478275.tsv
│           ├── logs
│           │   ├── GCF_900478275.log
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               └── GCF_900478275_GCF_900478275.gbk.gz
└── bactopia-runs
    └── phispy-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── phispy-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── phispy.tsv
        └── nf-reports
            ├── phispy-dag.dot
            ├── phispy-report.html
            └── phispy-timeline.html

Per-Sample Results

File	Description
*.txt	Tab-delimited file containing prophage predictions

Merged Results

File	Description
phispy.tsv	Merged TSV file containing prophage predictions from all samples

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
phispy-dag.dot	The Nextflow DAG visualization
phispy-report.html	The Nextflow Execution Report
phispy-timeline.html	The Nextflow Timeline Report
phispy-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

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

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• phispy - Prediction of prophages from bacterial 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