bakta_run

Tags: bacteria annotation genome assembly prodigal compliant genbank ena sample-scope

Rapid and standardized annotation of bacterial genomes and plasmids.

Uses Bakta to annotate genomes via alignment-free sequence identification. It detects CDS, sORFs, tRNAs, tmRNAs, rRNAs, ncRNAs, and CRISPR arrays, assigning functions from a comprehensive database.

Database Required

Requires a Bakta database (directory or tarball) to be available.

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
proteins: Path?
prodigal_tf: Path?
replicons: Path?

Name	Type	Description
db	Path	Path to the Bakta database (Directory or compressed tarball)
proteins	Path?	FASTA file of trusted proteins to use for first-pass annotation
prodigal_tf	Path?	Prodigal training file for CDS prediction
replicons	Path?	Table (TSV/CSV) of replicon information for origin detection

Outputs

record (
    meta: Record,
    blastdb: Path,
    faa: Path,
    ffn: Path,
    fna: Path,
    gbff: Path,
    gff: Path,
    hypotheticals_tsv: Path,
    hypotheticals_faa: Path,
    inference_tsv: Path,
    json: Path,
    png: Path,
    svg: Path,
    tsv: Path,
    txt: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
blastdb	Path	A compressed tar.gz archive of BLAST+ databases of the contigs, genes, and proteins
faa	Path	CDS/sORF amino acid sequences as FASTA
ffn	Path	Feature nucleotide sequences as FASTA
fna	Path	Replicon/contig DNA sequences as FASTA
gbff	Path	Annotations and sequences in GenBank format
gff	Path	Annotations and sequences in GFF3 format
hypotheticals_tsv	Path	Further information on hypothetical protein CDS as tab-separated values
hypotheticals_faa	Path	Hypothetical protein CDS amino acid sequences as FASTA
inference_tsv	Path	Detailed annotation evidence and database hit information
json	Path	Machine-readable annotations and metadata in JSON format
png	Path	Circular genome plot as PNG image
svg	Path	Circular genome plot as SVG image
tsv	Path	Annotations as simple human readable tab-separated values
txt	Path	Broad summary of Bakta annotations
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

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)

Used By

Subworkflows

• bakta - Rapid bacterial genome annotation.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• bakta - Rapid annotation of bacterial genomes and plasmids.
• staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

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)

• Aragorn
  Laslett D, Canback B ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32(1):11-6 (2004)

• DIAMOND
  Buchfink B, Xie C, Huson DH Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 12, 59-60 (2015)

• HMMER
  Eddy SR Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011)

• Infernal
  Nawrocki EP, Eddy SR Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29(22), 2933-2935 (2013)

• Prodigal
  Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11.1 119 (2010)

Source

View source on GitHub

Version

BAKTA_RUN:
    - bakta: 1.12.0