Workflow Type: Galaxy
Checking expected species and contamination in bacterial isolate
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

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Views: 38 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:03

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