Workflow Type: Galaxy
Open
Frozen
Structural genome annotation with Helixer
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Helixer, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Romane Libouban
Tutorial Author(s): Romane LIBOUBAN, Anthony Bretaudeau
Funder(s): EuroScienceGateway
Inputs
ID | Name | Description | Type |
---|---|---|---|
Genome | #main/Genome | Genome input (fasta format) |
|
Steps
ID | Name | Description |
---|---|---|
1 | Helixer | Structural annotation step toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1 |
2 | compleasm | Compleam is described as a faster and more accurate reimplementation of Busco. toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0 |
3 | BUSCO | BSUCO assesses the quality of genomic data. The tool inspects the transcription sequences of predicted genes. toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
4 | Genome annotation statistics Helixer | Calculate statistics from a genome annotation in GFF3 format toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 |
5 | JBrowse | Visualization toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
BUSCO gff3 | #main/BUSCO gff3 | n/a |
|
BUSCO miniprot | #main/BUSCO miniprot | n/a |
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BUSCO missing | #main/BUSCO missing | n/a |
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BUSCO sum | #main/BUSCO sum | n/a |
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BUSCO summary image | #main/BUSCO summary image | n/a |
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BUSCO table | #main/BUSCO table | n/a |
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Helixer | #main/Helixer | n/a |
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JBrowse output | #main/JBrowse output | n/a |
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compleasm full table | #main/compleasm full table | n/a |
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compleasm full table busco | #main/compleasm full table busco | n/a |
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compleasm miniprot | #main/compleasm miniprot | n/a |
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compleasm translated protein | #main/compleasm translated protein | n/a |
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graphs helixer | #main/graphs helixer | n/a |
|
summary helixer | #main/summary helixer | n/a |
|
Version History
2.0 (latest) Created 9th Dec 2024 at 13:45 by Helena Rasche
Added/updated 4 files
Open
master
64dfadc
1.0 (earliest) Created 26th Aug 2024 at 14:08 by Helena Rasche
Added/updated 4 files
Frozen
1.0
6340b35
Creators and Submitter
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License
Activity
Views: 375 Downloads: 115
Created: 26th Aug 2024 at 14:08
Last updated: 9th Dec 2024 at 13:45
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