Workflow Type: Galaxy
Frozen
Stable
The workflow requires the user to provide:
- ENSEMBL link address of the annotation GFF3 file
- ENSEMBL link address of the assembly FASTA file
- NCBI taxonomy ID
- BUSCO lineage
- OMArk database
Thw workflow will produce statistics of the annotation based on AGAT, BUSCO and OMArk.
Inputs
ID | Name | Description | Type |
---|---|---|---|
BUSCO Lineage | #main/BUSCO Lineage | Choose the (eukaryotic) BUSCO lineage that corresponds to the assembled species. EXAMPLE: mammalia_odb10 |
|
Enter GFF3 ENSEMBL link | #main/Enter GFF3 ENSEMBL link | EXAMPLE: https://ftp.ensembl.org/pub/rapid-release/species/Apodemus_agrarius/GCA_964023405.1/ensembl/geneset/2024_05/Apodemus_agrarius-GCA_964023405.1-2024_05-genes.gff3.gz |
|
Enter NCBI taxonomy ID | #main/Enter NCBI taxonomy ID | EXAMPLE: 39030 (Can be obtained from: https://www.ncbi.nlm.nih.gov/taxonomy) |
|
Enter genome ENSEMBL link | #main/Enter genome ENSEMBL link | EXAMPLE: https://ftp.ensembl.org/pub/rapid-release/species/Apodemus_agrarius/GCA_964023405.1/ensembl/genome/Apodemus_agrarius-GCA_964023405.1-unmasked.fa.gz |
|
Select OMArk database | #main/Select OMArk database | n/a |
|
Steps
ID | Name | Description |
---|---|---|
5 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
6 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
7 | downloads | lftp |
8 | downloads | lftp |
9 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
10 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
11 | AGAT | toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy2 |
12 | AGAT | toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy1 |
13 | AGAT | toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy1 |
14 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
15 | OMArk | toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2 |
Version History
Version 1 (earliest) Created 9th Aug 2024 at 15:14 by Diego De Panis
Initial commit
Frozen
Version-1
c0ef3ff
Creators and Submitter
Creator
Additional credit
ERGA
Submitter
Discussion Channel
Citation
De Panis, D. (2024). ERGA-BGE Genome Report ANNOT analyses. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1096.1
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Views: 867 Downloads: 115 Runs: 5
Created: 9th Aug 2024 at 15:14
Last updated: 20th Aug 2024 at 14:47
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