Checking expected species and contamination in bacterial isolate
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Run on GalaxyChecking 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
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Pierre, Bérénice Batut, Tristan Reynolds
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Clea Siguret, Tristan Reynolds, Helena Rasche, Saskia Hiltemann
Funder(s): ABRomics, The University of Melbourne, Melbourne Bioinformatics, Australian BioCommons
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input Paired End Reads Collection | #main/Input Paired End Reads Collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 |
| 2 | Bracken | toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 |
| 3 | Recentrifuge | toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+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
2.0
Creators and Submitter
Views: 2191 Downloads: 374 Runs: 1
Created: 2nd Jun 2025 at 11:03
Last updated: 22nd Dec 2025 at 13:13
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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