Galaxy |

Prokka (version 1.14.6+galaxy1)

Contigs to annotate:

FASTA format

Locus tag prefix:

Locus tag counter increment:

GFF version:

Force GenBank/ENA/DDJB compliance:

Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)

Add 'gene' features for each 'CDS' feature (--addgenes):

Minimum contig size (--mincontiglen):

NCBI needs 200

Sequencing centre ID:

Genus name:

May be used to aid annotation, see --usegenus below

Species name:

Strain name:

Plasmid name or identifier:

Kingdom:

(--kingdom)

Genetic code (transl_table):

Use genus-specific BLAST database:

Will use the BLAST database for the genus specified above, if installed

Optional FASTA file of trusted proteins to first annotate from:

Improve gene predictions for highly fragmented genomes:

Will set --meta option for Prodigal

Fast mode:

Skip CDS /product searching

Similarity e-value cut-off:

Enable searching for ncRNAs with Infernal+Rfam (SLOW!):

Don't run rRNA search with Barrnap:

Don't run tRNA search with Aragorn:

Additional outputs:

What it does

Prokka is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.

Output files

Prokka creates several output files, which are described in the Additional outputs section above.

License and citation

You can use this tool only if you agree to the license terms of: Prokka.