Workflow Type: Galaxy
Identification of AMR genes in an assembled bacterial genome
Associated Tutorial
This workflows is part of the tutorial Identification of AMR genes in an assembled bacterial genome, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bazante Sanders, Bérénice Batut
Tutorial Author(s): Bazante Sanders, Bérénice Batut
Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou, Deepti Varshney, pimarin, Bérénice Batut, Anthony Bretaudeau, Björn Grüning
Funder(s): Avans Hogeschool, ABRomics, ELIXIR Europe
Inputs
ID | Name | Description | Type |
---|---|---|---|
contigs | contigs | n/a |
|
forward_reads | forward_reads | n/a |
|
reverse_reads | reverse_reads | n/a |
|
Steps
ID | Name | Description |
---|---|---|
3 | staramr | toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 |
4 | Bakta | toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 |
5 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0 |
6 | Select | Grep1 |
7 | Table to GFF3 | toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 |
8 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
stararm_detailed_summary | stararm_detailed_summary | n/a |
|
bakta_annotation_summary | bakta_annotation_summary | n/a |
|
bowtie_mapping_stats | bowtie_mapping_stats | n/a |
|
jbrowse_output | jbrowse_output | n/a |
|
Version History

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Views: 42 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:55

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