defensefinder

Tags: anti-phage defense-systems hmm protein-domains bactopia-tool

Systematic identification of anti-phage defense systems.

This Bactopia Tool uses DefenseFinder to systematically search for and identify all known anti-phage defense systems in bacterial genomes using HMM-based protein domain detection.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── defensefinder-<TIMESTAMP>
│           ├── <SAMPLE_NAME>_defense_finder_genes.tsv
│           ├── <SAMPLE_NAME>_defense_finder_hmmer.tsv
│           ├── <SAMPLE_NAME>_defense_finder_systems.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── defensefinder-<TIMESTAMP>
        ├── merged-results
        │   ├── defensefinder-genes.tsv
        │   ├── defensefinder-hmmer.tsv
        │   ├── defensefinder-systems.tsv
        │   └── logs
        │       ├── defensefinder-genes-concat
        │       │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │       │   └── versions.yml
        │       ├── defensefinder-hmmer-concat
        │       │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │       │   └── versions.yml
        │       └── defensefinder-systems-concat
        │           ├── nf.command.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── defensefinder-dag.dot
            ├── defensefinder-report.html
            └── defensefinder-timeline.html

Per-Sample Results

File	Description
*.prt	FASTA file containing all proteins found in defense systems
*.prt.idx	Index file for the proteins file
*defense_finder_genes.tsv	TSV file with each gene found in defense systems
*defense_finder_hmmer.tsv	TSV file with each HMM hit
*defense_finder_systems.tsv	TSV file with information about each system found
*.macsydata.tar.gz	Raw MACSyFinder output file (requires --defensefinder_preserveraw)

Merged Results

File	Description
defensefinder-genes.tsv	Merged TSV of all genes found in defense systems
defensefinder-hmmer.tsv	Merged TSV of all HMM hits
defensefinder-systems.tsv	Merged TSV of all information about systems found

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
defensefinder-dag.dot	The Nextflow DAG visualization
defensefinder-report.html	The Nextflow Execution Report
defensefinder-timeline.html	The Nextflow Timeline Report
defensefinder-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

defense-finder Parameters

Parameter	Type	Default	Description
--defensefinder_coverage	number	0.4	Minimal percentage of coverage for each profiles
--defensefinder_dbtype	string	ordered_replicon	The macsyfinder --db-type option (choices: ordered_replicon, gembase, unordered)

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:

• defensefinder - Systematically search for anti-phage defense systems.

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)

• DefenseFinder
  Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, Bernheim A Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications, 13(1), 2561. (2022)

Source

View source on GitHub