Workflow Type: Galaxy

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

For this workflow:


  • assembled-genome.fasta
  • hard-repeat-masked-genome.fasta
  • If using the mRNAs option, the additional inputs required are .cdna, .pro and .dat files.

What it does:

  • This workflow splits the input genomes into single sequences (to decrease computation time), annotates using FgenesH++, and merges the output.


  • genome annotation in gff3 format
  • fasta files of mRNAs, cDNAs and proteins
  • Busco report


ID Name Description
0 assembled_genome.fasta fgenesh_split
1 repeat_masked_genome.fasta fgenesh_split
2 FGENESH annotate fgenesh_annotate
3 Merge into a single annotation file fgenesh_merge
4 FGENESH merge fgenesh_merge
5 FGENESH get mRNA or GC fgenesh_get_mrnas_gc
6 FGENESH get mRNA or GC fgenesh_get_mrnas_gc
7 FGENESH get protein fgenesh_get_proteins
8 Busco

Version History

Version 2.2 (latest) Created 18th Jun 2024 at 10:46 by Anna Syme

Adding .ga file

Frozen Version-2.2 76451e8

Version 2.1 Created 18th Jun 2024 at 10:08 by Anna Syme

add updated workflow image

Frozen Version-2.1 3cebff9

Version 2 Created 18th Jun 2024 at 09:56 by Anna Syme

Updated some labelling for clarity

Frozen Version-2 1b30a7e

Version 1 (earliest) Created 8th May 2024 at 08:28 by Anna Syme

Initial commit

Frozen Version-1 1b30a7e
help Creators and Submitter
  • Luke Silver
Silver, L. (2024). Fgenesh annotation -TSI. WorkflowHub.

Views: 956   Downloads: 146

Created: 8th May 2024 at 08:28

Last updated: 18th Jun 2024 at 09:59

help Attributions


Total size: 203 KB
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