annotation_helixer
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Download RO-CrateThis 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
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 (latest) Created 9th Dec 2024 at 13:45 by Helena Rasche
Added/updated 4 files
Open
master64dfadc
1.0 (earliest) Created 26th Aug 2024 at 14:08 by Helena Rasche
Added/updated 4 files
Frozen
1.06340b35
Creators and Submitter
Views: 376 Downloads: 116
Created: 26th Aug 2024 at 14:08
Last updated: 9th Dec 2024 at 13:45
Tags AttributionsNone
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