Workflow Type: Galaxy
Frozen
This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Augustus training | Augustus training | Augustus training |
|
BUSCO lineage | BUSCO lineage | BUSCO lineage |
|
Genome assembly | Genome assembly | Genome assembly |
|
Genome sequence | Genome sequence | Genome sequence |
|
Protein sequences | Protein sequences | Protein sequences |
|
SNAP training | SNAP training | SNAP training |
|
Steps
ID | Name | Description |
---|---|---|
6 | Fasta Statistics | Fasta Statistics on the genome toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
7 | BUSCO on the genome sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
8 | Maker | Annotation with Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11+galaxy2 |
9 | GFFRead | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
10 | Genome annotation statistics | Genome annotation statistics on the maker's annotation toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 |
11 | Map annotation ids | toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11 |
12 | BUSCO on the predicted protein sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
13 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
fasta stats genome | fasta stats genome | n/a |
|
busco image genome | busco image genome | n/a |
|
busco sum genome | busco sum genome | n/a |
|
busco table genome | busco table genome | n/a |
|
busco gff genome | busco gff genome | n/a |
|
busco missing genome | busco missing genome | n/a |
|
maker full | maker full | n/a |
|
maker gff | maker gff | n/a |
|
maker evidences | maker evidences | n/a |
|
gffread exons | gffread exons | n/a |
|
graphs genome | graphs genome | n/a |
|
summary genome | summary genome | n/a |
|
renamed gff3 | renamed gff3 | n/a |
|
id map | id map | n/a |
|
busco missing predicted proteins | busco missing predicted proteins | n/a |
|
busco table predicted proteins | busco table predicted proteins | n/a |
|
busco gff predicted proteins | busco gff predicted proteins | n/a |
|
busco sum predicted proteins | busco sum predicted proteins | n/a |
|
busco image predicted proteins | busco image predicted proteins | n/a |
|
jbrowse | jbrowse | n/a |
|
Version History
v0.1 (earliest) Created 26th Mar 2025 at 09:50 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
09ce1ab

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Views: 31 Downloads: 2 Runs: 0
Created: 26th Mar 2025 at 09:50

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