Bakta

The bakta module 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.

Output Overview

Below is the default output structure for the bakta step in Bactopia. Where possible the file descriptions below were modified from a tools description.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── main
│       └── annotator
│           └── bakta
│               ├── <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>.tsv
│               ├── <SAMPLE_NAME>.txt
│               └── logs
│                   ├── nf-bakta.{begin,err,log,out,run,sh,trace}
│                   └── versions.yml
└── bactopia-runs
    └── bakta-<TIMESTAMP>
        └── nf-reports
            ├── bakta-dag.dot
            ├── bakta-report.html
            ├── bakta-timeline.html
            └── bakta-trace.txt

Results

Bakta

Below is a description of the per-sample results from Bakta.

Extension	Description
.blastdb.tar.gz	A gzipped tar archive of BLAST+ database of the contigs, genes, and proteins
.embl.gz	Annotations & sequences in (multi) EMBL format
.faa.gz	CDS/sORF amino acid sequences as FASTA
.ffn.gz	Feature nucleotide sequences as FASTA
.fna.gz	Replicon/contig DNA sequences as FASTA
.gbff.gz	Annotations & sequences in (multi) GenBank format
.gff3.gz	Annotations & sequences in GFF3 format
.hypotheticals.faa.gz	Hypothetical protein CDS amino acid sequences as FASTA
.hypotheticals.tsv	Further information on hypothetical protein CDS as simple human readable tab separated values
.tsv	Annotations as simple human readable tab separated values
.txt	Broad summary of Bakta annotations

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

Parameters

Bakta Download

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

Bakta

Parameter	Description
--proteins	FASTA file of trusted proteins to first annotate from Type: string
--prodigal_tf	Training file to use for Prodigal Type: string
--replicons	Replicon information table (tsv/csv) Type: string
--min_contig_length	Minimum contig size to annotate Type: integer, Default: 1
--keep_contig_headers	Keep original contig headers Type: boolean
--compliant	Force Genbank/ENA/DDJB compliance Type: boolean
--skip_trna	Skip tRNA detection & annotation Type: boolean
--skip_tmrna	Skip tmRNA detection & annotation Type: boolean
--skip_rrna	Skip rRNA detection & annotation Type: boolean
--skip_ncrna	Skip ncRNA detection & annotation Type: boolean
--skip_ncrna_region	Skip ncRNA region detection & annotation Type: boolean
--skip_crispr	Skip CRISPR array detection & annotation Type: boolean
--skip_cds	Skip CDS detection & annotation Type: boolean
--skip_sorf	Skip sORF detection & annotation Type: boolean
--skip_gap	Skip gap detection & annotation Type: boolean
--skip_ori	Skip oriC/oriT detection & annotation Type: boolean
--bakta_opts	Extra Backa options in quotes. Example: '--gram +' Type: string

Citations

If you use Bactopia and bakta 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)