annotation-helixer/main
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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 |
|---|---|---|---|
| Genome sequence | #main/Genome sequence | 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/5.8.0+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/5.8.0+galaxy0 |
| 7 | OMArk | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| busco gff genome | #main/busco gff genome | n/a |
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| busco gff peptides | #main/busco gff peptides | n/a |
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| busco missing genome | #main/busco missing genome | n/a |
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| busco missing peptides | #main/busco missing peptides | n/a |
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| busco sum genome | #main/busco sum genome | n/a |
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| busco sum peptides | #main/busco sum peptides | n/a |
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| busco table genome | #main/busco table genome | n/a |
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| busco table peptides | #main/busco table peptides | n/a |
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| gffread peptides | #main/gffread peptides | n/a |
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| graphs | #main/graphs | n/a |
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| helixer output | #main/helixer output | n/a |
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| omark detail sum | #main/omark detail sum | n/a |
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| omark sum | #main/omark sum | n/a |
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| output | #main/output | n/a |
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| summary | #main/summary | n/a |
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| summary image genome | #main/summary image genome | n/a |
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| summary image peptides | #main/summary image peptides | 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: 266 Downloads: 52 Runs: 0
Created: 25th Jan 2025 at 03:01
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