Checking expected species and contamination in bacterial isolate 2.0
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Associated Tutorial
This workflows is part of the tutorial Checking expected species and contamination in bacterial isolate, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Pierre, Bérénice Batut
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Clea Siguret, Helena Rasche, Saskia Hiltemann
Funder(s): ABRomics
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| forward_reads | #main/forward_reads | forward_reads |
|
| reverse_reads | #main/reverse_reads | reverse_reads |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 |
| 3 | Bracken | toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 |
| 4 | Recentrifuge | toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| bracken_kraken_report | #main/bracken_kraken_report | n/a |
|
| bracken_report_tsv | #main/bracken_report_tsv | n/a |
|
| kraken_report_reads | #main/kraken_report_reads | n/a |
|
| kraken_report_tabular | #main/kraken_report_tabular | n/a |
|
| recentrifuge_data_tabular | #main/recentrifuge_data_tabular | n/a |
|
| recentrifuge_logfile | #main/recentrifuge_logfile | n/a |
|
| recentrifuge_report_html | #main/recentrifuge_report_html | n/a |
|
| recentrifuge_stats_tabular | #main/recentrifuge_stats_tabular | n/a |
|
Version History
master
Creators and Submitter
Views: 38 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:03
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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