Annotation Workflow

The Annotation workflow allows you to run selected annotation tools on an assembled genome (FASTA) without performing trimming or assembly.

Input

• A FASTA file containing assembled contigs or a complete genome
• Accepted extensions: .fasta, .fa, .fna

Available Tools

Select any combination of the following tools:

Tool	Description	Default
Prokka	Rapid prokaryotic gene annotation (CDS, rRNA, tRNA, tmRNA)	On
MLST	Multi-locus sequence typing against PubMLST databases	On
Barrnap	Ribosomal RNA gene prediction (5S, 16S, 23S)	On
Abricate	Antimicrobial resistance gene screening against multiple databases	On
AMRFinderPlus	NCBI's AMR gene and point mutation detection	Off
PlasmidFinder	Plasmid replicon identification	Off
MOB-suite	Plasmid classification and typing	Off
CRISPRCasFinder	CRISPR array and Cas gene detection	Off
tRNAscan-SE	Transfer RNA gene prediction	Off
Phigaro	Prophage region detection	Off
Kleborate	Klebsiella-specific virulence and resistance typing (only for Klebsiella)	Off
KOFAM	KEGG Orthology functional annotation	Off

Output Files

Each tool produces output in the job's predicted/ directory:

• Prokka: .gff (annotations), .gbk (GenBank), .faa (proteins), .ffn (genes), .txt (summary)
• MLST: .tsv with sequence type and allele profile
• Barrnap: .gff with rRNA gene locations
• Abricate: .tsv with resistance gene hits, coverage, and identity
• AMRFinderPlus: .tsv with AMR genes and point mutations

Parameters

Parameter	Required	Description
Genus	Yes	Organism genus (used by Prokka for annotation)
Species	Yes	Organism species
Sample Name	Yes	Name for the analysis run

Tip

You can type a custom genus or species if yours isn't in the dropdown list.

Note

Kleborate only runs when the genus is set to "Klebsiella".