annotation_helixer 2.0
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Run on GalaxyThis workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Helixer, 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, Anthony Bretaudeau
Tutorial Contributor(s): Felicitas Kindel, Björn Grüning, Anthony Bretaudeau, Helena Rasche, Romane LIBOUBAN, Saskia Hiltemann, Bérénice Batut
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input | #main/Input | Input dataset containing genomic sequences in FASTA format |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Helixer | Helixer tool for genomic annotation toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1 |
| 2 | Busco on genome | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 3 | Gffread | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 4 | Genome annotation statistics | Generates statistics and graphs for genome annotation toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 |
| 5 | JBrowse | JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 6 | Busco on protein | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 7 | OMArk | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| busco_gff_geno | #main/busco_gff_geno | n/a |
|
| busco_gff_pep | #main/busco_gff_pep | n/a |
|
| busco_missing_geno | #main/busco_missing_geno | n/a |
|
| busco_missing_pep | #main/busco_missing_pep | n/a |
|
| busco_sum_geno | #main/busco_sum_geno | n/a |
|
| busco_sum_pep | #main/busco_sum_pep | n/a |
|
| busco_table_geno | #main/busco_table_geno | n/a |
|
| busco_table_pep | #main/busco_table_pep | n/a |
|
| gffread_pep | #main/gffread_pep | n/a |
|
| graphs | #main/graphs | n/a |
|
| helixer_output | #main/helixer_output | n/a |
|
| omark_detail_sum | #main/omark_detail_sum | n/a |
|
| output | #main/output | n/a |
|
| summary | #main/summary | n/a |
|
| summary_image_geno | #main/summary_image_geno | n/a |
|
| summary_image_pep | #main/summary_image_pep | n/a |
|
Version History
2.0
Creators and Submitter
Views: 1584 Downloads: 211 Runs: 0
Created: 2nd Jun 2025 at 10:56
Last updated: 28th Jul 2025 at 11:11
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