gamma
Tags: gene allele mutation variant antimicrobial-resistance sample-scope
Gene Allele Mutation Microbial Assessment.
This subworkflow performs rapid identification, classification, and annotation of translated gene matches from sequencing data using GAMMA. The tool screens input sequences against a protein database to identify gene variants, mutations, and allele types, providing detailed annotation and classification.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for gene allele identification |
db: Path
| Name | Type | Description |
|---|---|---|
db | Path | Protein database file for sequence comparison (required) |
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 |
|---|---|
gamma | Main GAMMA output file containing annotated gene matches |
psl | Raw alignment details in PSL format |
gff | Gene matches in GFF3 format |
fasta | Extracted nucleotide sequences of the matched genes |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- gamma - Identification, classification, and annotation of translated gene matches.
Used By
This subworkflow is used by the following workflows:
- gamma - Identification, classification, and annotation of translated gene matches.
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) -
GAMMA
Stanton RA, Vlachos N, Halpin AL GAMMA: a tool for the rapid identification, classification, and annotation of translated gene matches from sequencing data. Bioinformatics (2021)