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

gff

meta:map

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

]

${prefix}/*.gff:file

annotation in GFF3 format, containing both sequences and annotations

*.{gff}

gbk

meta:map

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

]

${prefix}/*.gbk:file

annotation in GenBank format, containing both sequences and annotations

*.{gbk}

fna

meta:map

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

]

${prefix}/*.fna:file

nucleotide FASTA file of the input contig sequences

*.{fna}

faa

meta:map

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

]

${prefix}/*.faa:file

protein FASTA file of the translated CDS sequences

*.{faa}

ffn

meta:map

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

]

${prefix}/*.ffn:file

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

*.{ffn}

sqn

meta:map

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

]

${prefix}/*.sqn:file

an ASN1 format “Sequin” file for submission to Genbank

*.{sqn}

fsa

meta:map

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

]

${prefix}/*.fsa:file

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

*.{fsa}

tbl

meta:map

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

]

${prefix}/*.tbl:file

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

*.{tbl}

err

meta:map

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

]

${prefix}/*.err:file

unacceptable annotations - the NCBI discrepancy report.

*.{err}

log

meta:map

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

]

${prefix}/*.log:file

contains all the output that Prokka produced during its run

*.{log}

txt

meta:map

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

]

${prefix}/*.txt:file

statistics relating to the annotated features found

*.{txt}

tsv

meta:map

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

]

${prefix}/*.tsv:file

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

*.{tsv}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

prokka
GPL v2

Rapid annotation of prokaryotic genomes