mrsa AMR gene detection
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Run on GalaxyIdentification of AMR genes in an assembled bacterial genome
Associated Tutorial
This workflows is part of the tutorial mrsa AMR gene detection, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bazante Sanders, Bérénice Batut
Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou
Workflow Author(s): Bazante Sanders, Bérénice Batut
Funder(s): Avans Hogeschool, ABRomics
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
1.0 (latest) Created 16th Jul 2024 at 14:04 by Helena Rasche
Added/updated 4 files
Open
masteredb880e
4.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche
Added/updated 4 files
Frozen
4.084ada6d
Creators and Submitter
Views: 1446 Downloads: 538 Runs: 0
Created: 25th Jun 2024 at 11:05
Last updated: 25th Jun 2024 at 11:05
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
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