Bacterial Genome Annotation 2.0
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Associated Tutorial
This workflows is part of the tutorial Bacterial Genome Annotation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, Pierre Marin
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Helena Rasche, Bérénice Batut, Teresa Müller, Paul Zierep, Anthony Bretaudeau, Björn Grüning
Funder(s): ABRomics, ELIXIR Europe, Institut Français de Bioinformatique
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| contigs | contigs | contigs |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | ISEScan | toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 |
| 2 | PlasmidFinder | toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 |
| 3 | Integron Finder | toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 |
| 4 | Bakta | toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 |
| 5 | Group | Grouping1 |
| 6 | Group | Grouping1 |
| 7 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 8 | Select last | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 |
| 9 | Table to GFF3 | toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 |
| 10 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| isescan_results | isescan_results | n/a |
|
| plasmidfinder_results | plasmidfinder_results | n/a |
|
| integronfinder_summary | integronfinder_summary | n/a |
|
| bakta_summary | bakta_summary | n/a |
|
Version History
master
Creators and Submitter
Views: 42 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 10:56
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Teams: Galaxy Training Network
Organizations: Galaxy
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