Taxonomic Profiling and Visualization of Metagenomic Data 1.0
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Download RO-CrateTaxonomic Profiling and Visualization of Metagenomic Data
Associated Tutorial
This workflows is part of the tutorial Taxonomic Profiling and Visualization of Metagenomic Data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Sophia Hampe, Bérénice Batut, Paul Zierep
Workflow Author(s): Bérénice Batut
Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| metadata | metadata | n/a |
|
| raw-reads | raw-reads | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Unzip collection | __UNZIP_COLLECTION__ |
| 3 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 |
| 4 | MetaPhlAn | toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1 |
| 5 | Krakentools: Convert kraken report file | toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0 |
| 6 | Kraken-biom | toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 |
| 7 | Pavian | interactive_tool_pavian |
| 8 | Estimate Abundance at Taxonomic Level | toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy1 |
| 9 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 10 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 11 | Phinch Visualisation | interactive_tool_phinch |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| kraken_report | kraken_report | n/a |
|
| metaphlan_output | metaphlan_output | n/a |
|
| krakentool_report | krakentool_report | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 10:57 by Helena Rasche
Added/updated 4 files
Open
masterdd57c53
Creators and Submitter
Views: 264 Downloads: 81
Created: 25th Jun 2024 at 10:56
Last updated: 25th Jun 2024 at 10:57
Tags AttributionsNone
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