Taxonomic Profiling and Visualization of Metagenomic Data
2.0

Workflow Type: Galaxy

This 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

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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
metadata metadata n/a
  • File
raw-reads raw-reads n/a
  • File[]

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
  • File
krakentool_report krakentool_report n/a
  • File

Version History

2.0 (earliest) Created 2nd Jun 2025 at 10:54 by GTN Bot

Added/updated 4 files


Open master 5d1ebf5
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Created: 2nd Jun 2025 at 10:54

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