qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis
v0.1

View on GitHub Download RO-Crate Run on Galaxy
Workflow Type: Galaxy

This workflow

  • Reconstruct phylogeny (insert fragments in a reference)
  • Alpha rarefaction analysis
  • Taxonomic analysis

SEEK ID: https://workflowhub.eu/workflows/1090?version=1

Inputs

ID Name Description Type
Feature table #main/Feature table Feature table. e.g. from DADA2
  • File
Maximum depth #main/Maximum depth Maximum depth used for the rarefaction analysis (minimum value : 1)
  • int
Metadata #main/Metadata Tab separated metadata file
  • File
Minimum depth #main/Minimum depth Minimum depth used for the rarefaction analysis (minimum value : 1)
  • int
Representative sequences #main/Representative sequences Representative sequences, e.g. from DADA2
  • File
SEPP fragment insertion reference #main/SEPP fragment insertion reference Reference data for the SEPP fragmentation insertion phylogenetic tree generation
  • File
Taxonomic classifier #main/Taxonomic classifier Taxonomic classifier (e.g. Greengenes or SILVA)
  • File

Steps

ID Name Description
7 Phylogenetic tree for diversity analysis Phylogenetic tree for diversity analysis
8 Taxonomic analysis Taxonomic analysis
9 Rarefaction Rarefaction

Outputs

ID Name Description Type
Rarefaction curve #main/Rarefaction curve n/a
  • File
Rooted tree #main/Rooted tree n/a
  • File
Taxa barplot #main/Taxa barplot n/a
  • File
Taxonomy classification #main/Taxonomy classification n/a
  • File
Taxonomy classification table #main/Taxonomy classification table n/a
  • File

Version History

v0.1 (earliest) Created 7th Aug 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 76b5394
help Creators and Submitter
Creator
  • Debjyoti Ghosh
Additional credit

Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter
License
MIT License
Activity

Views: 619   Downloads: 108   Runs: 0

Created: 7th Aug 2024 at 03:02

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 116 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH