prokka - rapid annotation of prokaryotic genomes
- Prokka 1.10 by Torsten Seemann <torsten.seemann@monash.edu>
- rapid bacterial genome annotation
- prokka [options] <contigs.fasta>
- --outdir
[X]
- Output folder [auto] (default '')
- --force
- Force overwriting existing output folder (default OFF)
- --prefix
[X]
- Filename output prefix [auto] (default '')
- --addgenes
- Add 'gene' features for each 'CDS' feature (default OFF)
- --locustag
[X]
- Locus tag prefix (default 'PROKKA')
- --increment
[N]
- Locus tag counter increment (default '1')
- --gffver
[N]
- GFF version (default '3')
- --compliant
- Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen
200 --centre XXX (default OFF)
- --centre
[X]
- Sequencing centre ID. (default '')
- --kingdom
[X]
- Annotation mode: (default 'Bacteria')
- --gcode [N]
- Genetic code / Translation table (set if --kingdom is set) (default
'0')
- --gram [X]
- Gram: -/neg +/pos (default '')
- --usegenus
- Use genus-specific BLAST databases (needs --genus) (default
OFF)
- --proteins
[X]
- Fasta file of trusted proteins to first annotate from (default '')
- --metagenome
- Improve gene predictions for highly fragmented genomes (default OFF)
- --rawproduct
- Do not clean up /product annotation (default OFF)
- --fast
- Fast mode - skip CDS /product searching (default OFF)
- --cpus [N]
- Number of CPUs to use [0=all] (default '8')
--mincontiglen [N] Minimum contig size [NCBI needs 200]
(default '1')
- --evalue
[n.n]
- Similarity e-value cut-off (default '1e-06')
- --rfam
- Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
- --norrna
- Don't run rRNA search (default OFF)
- --notrna
- Don't run tRNA search (default OFF)
- --rnammer
- Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)