Taxonomy Profiling and Visualization with Krona
2.0

Workflow Type: Galaxy

Microbiome - Taxonomy Profiling

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

Thanks to...

Workflow Author(s): Engy Nasr, Bérénice Batut, Paul Zierep

Tutorial Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Tutorial Contributor(s): Hans-Rudolf Hotz, Wolfgang Maier, Saskia Hiltemann, Deepti Varshney, Paul Zierep, Bérénice Batut, Björn Grüning, Cristóbal Gallardo, Engy Nasr, Helena Rasche

Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EOSC-Life

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
collection_of_preprocessed_samples #main/collection_of_preprocessed_samples Output collection from the Nanopore Preprocessing workflow
  • array containing
    • File
kraken_database #main/kraken_database kraken_database_for_user_to_choose
  • string

Steps

ID Name Description
2 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
3 Krakentools: Convert kraken report file toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1
4 Krona pie chart toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0

Outputs

ID Name Description Type
converted_kraken_report #main/converted_kraken_report n/a
  • File
kraken2_with_pluspf_database_output #main/kraken2_with_pluspf_database_output n/a
  • File
kraken2_with_pluspf_database_output_report #main/kraken2_with_pluspf_database_output_report n/a
  • File
krona_pie_chart #main/krona_pie_chart n/a
  • File

Version History

2.0 (earliest) Created 2nd Jun 2025 at 10:55 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:55

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