annotation-helixer/main
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Tests This 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.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| BUSCO lineage | #main/BUSCO lineage | BUSCO lineage |
|
| Genome sequence masked | #main/Genome sequence masked | Genome sequence |
|
| Helixer lineage | #main/Helixer lineage | Helixer lineage |
|
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 | BUSCO on the genome sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 5 | Genome annotation statistics | Genome annotation statistics toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 |
| 6 | JBrowse | JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 7 | GFFRead | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 8 | OMArk | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.1+galaxy1 |
| 9 | BUSCO on the predicted protein sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| busco gff genome | #main/busco gff genome | n/a |
|
| busco gff predicted proteins | #main/busco gff predicted proteins | n/a |
|
| busco image predicted proteins | #main/busco image predicted proteins | n/a |
|
| busco missing genome | #main/busco missing genome | n/a |
|
| busco missing predicted proteins | #main/busco missing predicted proteins | n/a |
|
| busco sum genome | #main/busco sum genome | n/a |
|
| busco sum predicted proteins | #main/busco sum predicted proteins | n/a |
|
| busco table genome | #main/busco table genome | n/a |
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| busco table predicted proteins | #main/busco table predicted proteins | n/a |
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| gffread peptides | #main/gffread peptides | n/a |
|
| graphs | #main/graphs | n/a |
|
| helixer output | #main/helixer output | n/a |
|
| jbrowse | #main/jbrowse | n/a |
|
| omark detail sum | #main/omark detail sum | n/a |
|
| omark sum | #main/omark sum | n/a |
|
| summary | #main/summary | n/a |
|
| summary image genome | #main/summary image genome | n/a |
|
Version History
v0.1 (earliest) Created 25th Jan 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
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v0.18cc0bc4
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Views: 1912 Downloads: 360 Runs: 0
Created: 25th Jan 2025 at 03:01
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