Workflow 2: Community Profile
1.0

Workflow Type: Galaxy

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

Thanks to...

Workflow Author(s): Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep

Tutorial Author(s): Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr

Tutorial Contributor(s): Bérénice Batut, Helena Rasche, Saskia Hiltemann, Paul Zierep

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
QC controlled forward reads #main/QC controlled forward reads n/a
  • File
QC controlled reverse reads #main/QC controlled reverse reads n/a
  • File

Steps

ID Name Description
2 Taxonomic assignation toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0
3 Cut Cut1
4 Krona pie chart toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
5 Export to GraPhlAn toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0
6 Generation, personalization and annotation of tree toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0
7 Visualisation (GraPhlAn) toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0

Outputs

ID Name Description Type
Export to GraPhlAn on input dataset(s): Annotation #main/Export to GraPhlAn on input dataset(s): Annotation n/a
  • File
Export to GraPhlAn on input dataset(s): Tree #main/Export to GraPhlAn on input dataset(s): Tree n/a
  • File
Generation, personalization and annotation of tree on input dataset(s): Tree in PhyloXML #main/Generation, personalization and annotation of tree on input dataset(s): Tree in PhyloXML n/a
  • File
GraPhlAn on input dataset(s): PNG #main/GraPhlAn on input dataset(s): PNG n/a
  • File
MetaPhlAn on input dataset(s): BIOM file #main/MetaPhlAn on input dataset(s): BIOM file n/a
  • File
MetaPhlAn on input dataset(s): Bowtie2 output #main/MetaPhlAn on input dataset(s): Bowtie2 output n/a
  • File
MetaPhlAn on input dataset(s): Predicted taxon relative abundances #main/MetaPhlAn on input dataset(s): Predicted taxon relative abundances n/a
  • File
MetaPhlAn on input dataset(s): SAM file #main/MetaPhlAn on input dataset(s): SAM file n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:53 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:53

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