Workflow Type: Galaxy
Open
Frozen
Bacterial Genome Annotation
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
Funder(s): ABRomics
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
2.0 (latest) Created 5th Aug 2024 at 14:04 by Helena Rasche
Added/updated 4 files
Open
master
12446cd
1.0 (earliest) Created 25th Jun 2024 at 11:02 by Helena Rasche
Added/updated 4 files
Frozen
1.0
a59455f
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
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Discussion Channel
Activity
Views: 176 Downloads: 65
Created: 25th Jun 2024 at 11:02
Last updated: 5th Aug 2024 at 14:04
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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