Taxonomic Profiling and Visualization of Metagenomic Data
1.0

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Workflow Type: Galaxy

Taxonomic 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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1095?version=1

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/kraken2/2.1.1+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
  • File
metaphlan_output metaphlan_output n/a
  • File
krakentool_report krakentool_report n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:57 by Helena Rasche

Added/updated 4 files


Open master dd57c53
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
kraken2
MetaPhlAn
KrakenTools
Bracken
taxonomy_krona_chart
License
MIT License
Activity

Views: 130   Downloads: 48

Created: 25th Jun 2024 at 10:56

Last updated: 25th Jun 2024 at 10:57

help Attributions

None

Total size: 89.3 KB
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