Taxonomic Profiling and Visualization of Metagenomic Data
Version 1

Visit source Download RO Crate
Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/917?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 (earliest) Created 22nd Apr 2024 at 11:05 by Helena Rasche

Added/updated 3 files


Open master 1a2038a
help Creators and Submitter
Creator
  • Bérénice Batut
Submitter
Tools
kraken2
MetaPhlAn
KrakenTools
Bracken
taxonomy_krona_chart
License
MIT License
Activity

Views: 31

Created: 22nd Apr 2024 at 11:05

Last updated: 22nd Apr 2024 at 11:05

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help Attributions

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Total size: 23.6 KB
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