prokka

Tags: prokka annotation prokaryotic bacteria genbank gff sample-scope

Annotate prokaryotic genomes.

Uses Prokka to rapidly annotate bacterial, archaeal, and viral genomes, producing standards-compliant output files including GFF3, GenBank, and Sequin.

Inputs

record (
    meta: Record,
    fna: Path
)

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

proteins: Path?
prodigal_tf: Path?

Name	Type	Description
proteins	Path?	FASTA file of trusted proteins to first annotate from
prodigal_tf	Path?	Training file to use for gene prediction

Outputs

record (
    meta: Record,
    gff: Path,
    gbff: Path,
    fna: Path,
    faa: Path,
    ffn: Path,
    sqn: Path,
    fsa: Path,
    tbl: Path,
    txt: Path,
    tsv: Path,
    blastdb: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
gff	Path	Annotation in GFF3 format, containing both sequences and annotations
gbff	Path	Annotation in GenBank format, containing both sequences and annotations
fna	Path	Nucleotide FASTA file of the input contig sequences
faa	Path	Protein FASTA file of the translated CDS sequences
ffn	Path	Nucleotide FASTA file of all prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)
sqn	Path	An ASN1 format "Sequin" file for submission to GenBank
fsa	Path	Nucleotide FASTA file of the input contig sequences, used by tbl2asn
tbl	Path	Feature Table file for NCBI submission
txt	Path	Summary statistics relating to the annotated features found
tsv	Path	Tab-separated file of all features (locus_tag, ftype, len_bp, gene, EC_number, COG, product)
blastdb	Path	A compressed tar.gz archive of BLAST+ databases of the contigs, genes, and proteins
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

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

Used By

Subworkflows

• prokka - Annotate bacterial genomes with functional information.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• pangenome - Pangenome analysis with optional core-genome phylogeny.
• prokka - Rapid whole genome annotation of bacterial, archaeal, and viral genomes.
• 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)

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

• 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)

• Barrnap
  Seemann T Barrnap: Bacterial ribosomal RNA predictor (GitHub)

• CD-HIT
  Li W, Godzik A Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006)

• 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)

• MinCED
  Skennerton C MinCED: Mining CRISPRs in Environmental Datasets (GitHub)

• nhmmer
  Wheeler TJ, Eddy SR nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487-2489 (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)

• RNAmmer
  Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW RNAmmer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 35.9: 3100-3108 (2007)

• SignalP
  Petersen TN, Brunak S, von Heijne G, Nielsen H SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods 8.10: 785 (2011)

Source

View source on GitHub

Version

PROKKA:
    - prokka: 1.15.6