Description

Whole genome annotation of small genomes (bacterial, archeal, viral)

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

FASTA file to be annotated. Has to contain at least a non-empty string dummy value.

proteins (file)

FASTA file of trusted proteins to first annotate from (optional)

prodigal_tf (file)

Training file to use for Prodigal (optional)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

gff (file)

annotation in GFF3 format, containing both sequences and annotations

*.{gff}

gbk (file)

annotation in GenBank format, containing both sequences and annotations

*.{gbk}

fna (file)

nucleotide FASTA file of the input contig sequences

*.{fna}

faa (file)

protein FASTA file of the translated CDS sequences

*.{faa}

ffn (file)

nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)

*.{ffn}

sqn (file)

an ASN1 format “Sequin” file for submission to Genbank

*.{sqn}

fsa (file)

nucleotide FASTA file of the input contig sequences, used by “tbl2asn” to create the .sqn file

*.{fsa}

tbl (file)

feature Table file, used by “tbl2asn” to create the .sqn file

*.{tbl}

err (file)

unacceptable annotations - the NCBI discrepancy report.

*.{err}

log (file)

contains all the output that Prokka produced during its run

*.{log}

txt (file)

statistics relating to the annotated features found

*.{txt}

tsv (file)

tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)

*.{tsv}
included in
bacass funcscan mag metatdenovo
author
Github user rpetit3
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

prokka
GPL v2

Rapid annotation of prokaryotic genomes

github.com/tseemann/prokka 10.1093/bioinformatics/btu153