bakta

Tags: bacteria fasta annotation genbank gff proteins bactopia-tool

Rapid annotation of bacterial genomes and plasmids.

This Bactopia Tool uses Bakta to rapidly annotate bacterial genomes and plasmids in a standardized fashion. Bakta makes use of a large database (40+ GB) to provide extensive annotations including: tRNA, tmRNA, rRNA, ncRNA, CRISPR, CDS, and sORFs.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── main
│       └── annotator
│           └── bakta-<TIMESTAMP>
│               ├── <SAMPLE_NAME>-blastdb.tar.gz
│               ├── <SAMPLE_NAME>.embl.gz
│               ├── <SAMPLE_NAME>.faa.gz
│               ├── <SAMPLE_NAME>.ffn.gz
│               ├── <SAMPLE_NAME>.fna.gz
│               ├── <SAMPLE_NAME>.gbff.gz
│               ├── <SAMPLE_NAME>.gff3.gz
│               ├── <SAMPLE_NAME>.hypotheticals.faa.gz
│               ├── <SAMPLE_NAME>.hypotheticals.tsv
│               ├── <SAMPLE_NAME>.inference.tsv
│               ├── <SAMPLE_NAME>.json.gz
│               ├── <SAMPLE_NAME>.png
│               ├── <SAMPLE_NAME>.svg.gz
│               ├── <SAMPLE_NAME>.tsv
│               ├── <SAMPLE_NAME>.txt
│               └── logs
│                   ├── <SAMPLE_NAME>.log
│                   ├── nf.command.{begin,err,log,out,run,sh,trace}
│                   └── versions.yml
└── bactopia-runs
    └── bakta-<TIMESTAMP>
        └── nf-reports
            ├── bakta-dag.dot
            ├── bakta-report.html
            └── bakta-timeline.html

Annotation

File	Description
*.gff3	Genome annotation in GFF3 format
*.gbff	Genome annotation in GenBank format
*.faa	Protein sequences in FASTA format
*.ffn	Feature nucleotide sequences
*.fna	Nucleotide sequences of all features
*.hypotheticals.tsv	List of hypothetical proteins
*.tsv	Annotation summary in TSV format
*.txt	Detailed annotation report

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

Bakta Download Parameters

Parameter	Type	Default	Description
--bakta_db	string		Tarball or path to the Bakta database
--bakta_db_type	string	full	Which Bakta DB to download 'full' (~30GB) or 'light' (~2GB) (choices: full, light)
--bakta_save_as_tarball	boolean	false	Save the Bakta database as a tarball
--download_bakta	boolean	false	Download the Bakta database to the path given by --bakta_db

Bakta Parameters

Parameter	Type	Default	Description
--bakta_proteins	string		FASTA file of trusted proteins to first annotate from
--bakta_prodigal_tf	string		Training file to use for Prodigal
--bakta_replicons	string		Replicon information table (tsv/csv)

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:

• bakta - Rapid bacterial genome annotation.

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)

• Bakta
  Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A Bakta - rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics 7(11) (2021)

Source

View source on GitHub