gamma

Tags: gene-finding annotation homology alignment gamma psl sample-scope

Identification, classification, and annotation of translated gene matches.

Uses GAMMA (Gene Allele Mutation Microbial Assessment) to identify and annotate coding sequences in an assembly that match a specific gene database. It is particularly useful for detecting specific targets like antimicrobial resistance genes or virulence factors while accounting for potential mutations.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

db: Path

Name	Type	Description
db	Path	The reference gene database in FASTA format

Outputs

record (
    meta: Record,
    gamma: Path,
    psl: Path,
    gff: Path?,
    fasta: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
gamma	Path	Main GAMMA output file containing annotated gene matches
psl	Path	Raw alignment details in PSL format
gff	Path?	Gene matches in GFF3 format
fasta	Path?	Extracted nucleotide sequences of the matched genes
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

GAMMA Parameters

Parameter	Type	Default	Description
--gamma_db	string		A gene database (FASTA) for GAMMA
--gamma_percent_identity	integer	90	The minimum nucleotide sequence identity % used by the Blat search

Used By

Subworkflows

• gamma - Gene Allele Mutation Microbial Assessment.

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)

Source

View source on GitHub

Version

GAMMA:
    - gamma: 2.2