Funannotate functional (version 1.8.17+galaxy5)

Input format:

Genome annotation in genbank format:

Output from 'Funannotate predict annotation' tool

Funannotate database:

NCBI submission template file:

Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)

Eggnog-mapper annotations file:

'annotations' output from 'eggNOG Mapper' tool

antiSMASH secondary metabolism results:

Genbank output from 'Antismash' tool

InterProScan5 XML file:

XML output from InterProScan

Phobius pre-computed results:

BUSCO models:

Custom annotations:

3 column tsv file

Isolate name:

If relevant (e.g. Af293)

Strain name:

If relevant (e.g. FGSCA4)

locus_tag from NCBI to rename GFF gene models with:

Gene/Product names fixed:

TSV: GeneID Name Product

Gene/Product names to remove:

TSV: Gene Product

Maximum length of FASTA headers:

The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI.

Which outputs should be generated:

Funannotate annotate

Funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).

This script functionally annotates the results from funannotate predict. It pulls annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.