defensefinder
Tags: bacteria assembly anti-phage defense-systems immunity sample-scope
Systematically search for anti-phage defense systems.
This subworkflow uses DefenseFinder to identify and classify anti-phage defense systems in bacterial genomes. It detects defense genes, HMM hits, and complete defense systems, providing comprehensive analysis of bacterial antiviral mechanisms.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format for defense system detection |
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 |
|---|---|
genes_tsv | Tab-delimited list of detected defense genes |
hmmer_tsv | Tab-delimited list of HMMER hits used for detection |
systems_tsv | Tab-delimited summary of detected defense systems |
proteins | Protein sequences of the detected defense genes |
proteins_index | Index file for the protein sequences |
macsydata_raw | Compressed tarball of raw MacSyFinder data (optional) |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- defensefinder_run - Detect anti-phage defense systems using HMM profiles.
- defensefinder_update - Download and package the DefenseFinder and CasFinder model databases.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- defensefinder - Systematic identification of 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)