Fgenesh annotation -TSI
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Run on GalaxyThis 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:
Inputs:
- 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.
Outputs:
- genome annotation in gff3 format
- fasta files of mRNAs, cDNAs and proteins
- Busco report
Steps
| ID | Name | Description |
|---|---|---|
| 0 | FGENESH split | fgenesh_split |
| 1 | FGENESH split | fgenesh_split |
| 2 | FGENESH annotate | fgenesh_annotate |
| 3 | FGENESH merge | 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 | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
Version History
Version 3.2 (latest) Created 18th Apr 2026 at 11:50 by Anna Syme
Shortened the licence-agreement parameter input label from the full BioCommons acknowledgement text to "Licence agreement (tick to accept Fgenesh terms)" to tidy the workflow diagram. Updated the workflow description to accurately list inputs (assembled_genome.fasta, hard_masked_genome.fasta, mRNA_sequences.fasta) and clarify that species matrix, NR database and BUSCO lineage are dropdown selections rather than uploaded files. No functional changes; .ga steps and tool versions unchanged from Version 3.1.
Frozen
Version-3.2af61f4b
Version 3.1 Created 18th Apr 2026 at 11:21 by Anna Syme
Fixed: added license_agreements input, mRNA_sequences.fasta input, updated fgenesh_annotate/fgenesh_get_proteins to v2024.2+galaxy1. Tested on S. cerevisiae (BUSCO C:84.0%).
Frozen
Version-3.1
fe9c08f
Version 3 Created 17th Nov 2024 at 23:41 by Anna Syme
Changes made 13 Nov 2024: Added correct input files and connected them to the split steps. Added inputs for db selections in the annotation step. Added lineage input to Busco. Added genome annotation stats derived from gff3 output. Connected in assembly.fasta sequences to "get mRNA/cDNA" tools. Expanded this information text and clarified the need for .cdna .pro and .dat files as input.
Frozen
Version-3
fe9c08f
Version 2.1 Created 18th Jun 2024 at 10:08 by Anna Syme
add updated workflow image
Frozen
Version-2.1
3cebff9
Version 1 (earliest) Created 8th May 2024 at 08:28 by Anna Syme
Initial commit
Frozen
Version-1
1b30a7e
Creators and Submitter
Views: 9336 Downloads: 2487 Runs: 13
Created: 8th May 2024 at 08:28
Last updated: 18th Apr 2026 at 11:56
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https://orcid.org/0000-0002-9906-0673
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia, National Computational Infrastructure (NCI) WorkflowHub team
Web page: https://www.biocommons.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy ...
Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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
