Checking expected species and contamination in bacterial isolate
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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...
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Clea Siguret
Workflow Author(s): Pierre, Bérénice Batut
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
2.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche
Added/updated 4 files
Open
master15a562e
3.0 (earliest) Created 25th Jun 2024 at 11:11 by Helena Rasche
Added/updated 4 files
Frozen
3.0d7ec76d
Creators and Submitter
Views: 440 Downloads: 149
Created: 25th Jun 2024 at 11:11
Last updated: 25th Jun 2024 at 11:11
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
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