Taxonomic Profiling and Visualization of Metagenomic Data 2.0
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Run on GalaxyThis workflow performs taxonomic profiling of metagenomic data and visualizes microbial community composition using Kraken2 and Bracken as well as MetaPhlAn.
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
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Bérénice Batut, Tarnima Omara
Tutorial Author(s): Sophia Hampe, Bérénice Batut, Paul Zierep
Tutorial Contributor(s): Tarnima Omara, Saskia Hiltemann, Bérénice Batut, Paul Zierep, Helena Rasche, Cristóbal Gallardo, Teresa Müller
Grants(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/kraken2/2.1.3+galaxy1 |
| 4 | MetaPhlAn | toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 |
| 5 | Krakentools: Convert kraken report file | toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 |
| 6 | Kraken-biom | toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 |
| 7 | Pavian | interactive_tool_pavian |
| 8 | Bracken | toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 |
| 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 |
|---|---|---|---|
| metaphlan_output | metaphlan_output | n/a |
|
| krakentool_report | krakentool_report | n/a |
|
Version History
master
Creators and Submitter
Views: 47 Downloads: 5 Runs: 0
Created: 2nd Jun 2025 at 10:54
Tags AttributionsNone
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Organizations: Galaxy
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