Comparison of two annotation tools: Helixer and Braker3 1.0
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Run on GalaxyThe idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.
Associated Tutorial
This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Romane Libouban
Tutorial Author(s): Romane LIBOUBAN
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Alignments from RNA-seq | Alignments from RNA-seq | Alignments from RNA-seq |
|
| Genome sequence | Genome sequence | Input dataset containing genomic sequences in FASTA format |
|
| Protein sequences | Protein sequences | Protein sequences |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Helixer | Helixer tool for genomic annotation toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1 |
| 4 | Braker3 | Braker3 is an automated bioinformatics tool that uses RNA-seq and protein data to annotate genomes. toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy0 |
| 5 | Gffread Helixer annotation | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 6 | JBrowse | JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 7 | Gffread Braker3 annotation | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 8 | Busco on predicted proteins from Helixer annotation | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0 |
| 9 | OMArk on predicted proteins from Helixer annotation | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.1+galaxy0 |
| 10 | OMArk on predicted proteins from Braker3 annotation | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.1+galaxy0 |
| 11 | Busco on predicted proteins from Braker3 annotation | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| helixer output | helixer output | n/a |
|
| predicted proteins Helixer annotation | predicted proteins Helixer annotation | n/a |
|
| output | output | n/a |
|
| predicted proteins Braker3 annotation | predicted proteins Braker3 annotation | n/a |
|
| busco gff predicted proteins Helixer | busco gff predicted proteins Helixer | n/a |
|
| busco image predicted proteins Helixer | busco image predicted proteins Helixer | n/a |
|
| busco missing predicted proteins Helixer | busco missing predicted proteins Helixer | n/a |
|
| busco table predicted proteins Helixer | busco table predicted proteins Helixer | n/a |
|
| busco sum predicted proteins Helixer | busco sum predicted proteins Helixer | n/a |
|
| omark detail sum Helixer annotation | omark detail sum Helixer annotation | n/a |
|
| omark sum | omark sum | n/a |
|
| omark detail sum Braker3 annotation | omark detail sum Braker3 annotation | n/a |
|
| busco image predicted proteins Braker3 | busco image predicted proteins Braker3 | n/a |
|
| busco gff predicted proteins Braker3 | busco gff predicted proteins Braker3 | n/a |
|
| busco sum predicted proteins Braker3 | busco sum predicted proteins Braker3 | n/a |
|
| busco table predicted proteins Braker3 | busco table predicted proteins Braker3 | n/a |
|
| busco missing predicted proteins Braker3 | busco missing predicted proteins Braker3 | n/a |
|
Version History
1.0
Creators and Submitter
Views: 1123 Downloads: 196 Runs: 0
Created: 23rd Jun 2025 at 14:13
Last updated: 28th Jul 2025 at 10:54
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