PROKKA(1)

🦋 PROKKA — like, the manual, but make it make sense

okay bestie, welcome to PROKKA(1) — the man page. this is the whole thing, nothing skipped, no cap. grab a boba, we're annotating genomes. 💖

prokka — rapid annotation of prokaryotic genomes. that's the whole vibe. 🧬

Prokka 1.10 by Torsten Seemann <torsten.seemann@monash.edu> — yeah that's the author, show some respect. 👑

rapid bacterial genome annotation. that's it. that's the mission. periodt.

prokka [options] <contigs.fasta>

like, you give it contigs, it gives you annotations. iconic behavior.

--help — This help. when you're lost, ask for help. no shame.
--version — Print version and exit. like "who am i" but for the software.
--docs — Show full manual/documentation. the extended cut. director's commentary. 🎬
--citation — Print citation for referencing Prokka. cite it or it didn't happen, fr fr. 📚
--quiet — No screen output (default OFF). silent mode. main character energy with the mute button on. 🤫

--listdb — List all configured databases. inventory check. what do we have, bestie?
--setupdb — Index all installed databases. get them ready for their moment.
--cleandb — Remove all database indices. yeah we're deleting. it's giving spring cleaning. 🧹
--depends — List all software dependencies. the whole entourage. 👑

--outdir [X] — Output folder [auto] (default ''). where the magic lands.
--force — Force overwriting existing output folder (default OFF). destructive and unbothered. 💀 careful.
--prefix [X] — Filename output prefix [auto] (default ''). name your babies.
--addgenes — Add 'gene' features for each 'CDS' feature (default OFF). extra detail, we love to see it.
--locustag [X] — Locus tag prefix (default 'PROKKA'). the family name.
--increment [N] — Locus tag counter increment (default '1'). how fast we count up.
--gffver [N] — GFF version (default '3').
--compliant — Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF). the "follow the rules" bundle. 📋
--centre [X] — Sequencing centre ID. (default '').

--genus [X] — Genus name (default 'Genus').
--species [X] — Species name (default 'species').
--strain [X] — Strain name (default 'strain').
--plasmid [X] — Plasmid name or identifier (default ''). the little extra one. 🧫

--kingdom [X] — Annotation mode: (default 'Bacteria'). pick your kingdom. no monarchs required.
--gcode [N] — Genetic code / Translation table (set if --kingdom is set) (default '0').
--gram [X] — Gram: -/neg +/pos (default ''). the stain test. 🎨
--usegenus — Use genus-specific BLAST databases (needs --genus) (default OFF). fancy. needs the genus first tho.
--proteins [X] — Fasta file of trusted proteins to first annotate from (default ''). your trusted circle. 🫶
--metagenome — Improve gene predictions for highly fragmented genomes (default OFF).
--rawproduct — Do not clean up /product annotation (default OFF). leave it messy. chaos aesthetic.

--fast — Fast mode - skip CDS /product searching (default OFF). zoom zoom.
--cpus [N] — Number of CPUs to use [0=all] (default '8'). use the whole squad.
--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'). bestie it literally says SLOW in all caps, it's not playing. 😭
--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). picking favorites. 🙈

and that's the whole page, start to finish, no skips. 💜

this has been prokka 1.11, dated February 2015 — and PROKKA(1) says bye bestie, go annotate something gorgeous. ✨💅🦋

📦 where this page comes from