prokka

Tags: annotation genome prokaryote functional-annotation genes bactopia-tool

Rapid whole genome annotation of bacterial, archaeal, and viral genomes.

This Bactopia Tool uses Prokka to rapidly annotate small genomes in a standardized fashion. It identifies protein-coding genes, rRNA, tRNA, and other features, then searches them against multiple reference databases to provide comprehensive functional annotation.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── main
│       └── annotator
│           └── prokka-<TIMESTAMP>
│               ├── <SAMPLE_NAME>-blastdb.tar.gz
│               ├── <SAMPLE_NAME>.faa.gz
│               ├── <SAMPLE_NAME>.ffn.gz
│               ├── <SAMPLE_NAME>.fna.gz
│               ├── <SAMPLE_NAME>.fsa.gz
│               ├── <SAMPLE_NAME>.gbk.gz
│               ├── <SAMPLE_NAME>.gff.gz
│               ├── <SAMPLE_NAME>.sqn.gz
│               ├── <SAMPLE_NAME>.tbl.gz
│               ├── <SAMPLE_NAME>.tsv
│               ├── <SAMPLE_NAME>.txt
│               └── logs
│                   ├── <SAMPLE_NAME>.err
│                   ├── <SAMPLE_NAME>.log
│                   ├── nf.command.{begin,err,log,out,run,sh,trace}
│                   └── versions.yml
└── bactopia-runs
    └── prokka-<TIMESTAMP>
        └── nf-reports
            ├── prokka-dag.dot
            ├── prokka-report.html
            └── prokka-timeline.html

Per-Sample Results

File	Description
*.gff	Genome annotation in GFF3 format containing sequences and annotations
*.gbk	Genome annotation in GenBank format containing sequences and annotations
*.faa	Protein FASTA file of translated CDS sequences
*.fna	Nucleotide FASTA file of input contig sequences
*.ffn	Nucleotide FASTA file of all predicted transcripts
*.fsa	Nucleotide FASTA file of predicted protein sequences
*.sqn	ASN1 format Sequin file for GenBank submission
*.tbl	Feature Table file for GenBank submission
*.tsv	Tab-separated file of all features with functional information
*.txt	Statistics report of annotated features
*.blastdb.tar.gz	BLAST+ database archive of contigs, genes, and proteins

Merged Results

File	Description
prokka.tsv	Merged TSV file containing annotation summaries 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
prokka-dag.dot	The Nextflow DAG visualization
prokka-report.html	The Nextflow Execution Report
prokka-timeline.html	The Nextflow Timeline Report
prokka-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

Prokka Parameters

Parameter	Type	Default	Description
--prokka_proteins	string	${projectDir}/data/proteins.faa	FASTA file of trusted proteins to first annotate from
--prokka_prodigal_tf	string		Training file to use for Prodigal
--prokka_coverage	integer	80	Minimum coverage on query protein

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:

• prokka - Annotate bacterial genomes with functional information.

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)

• Prokka
  Seemann T Prokka: rapid prokaryotic genome annotation Bioinformatics 30, 2068-2069 (2014)

Source

View source on GitHub