Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]

microbiome-mothur-miseq-sop-short/workflow2-data-cleaning

Author(s)
Saskia Hiltemann
Version
1
Last updated
Jan 15, 2024
License
MIT
Tags
microbiome

Features
Tutorial
16S Microbial Analysis with mothur (short)
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00134
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nAligned Sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCount Table"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Summary.seqs"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Screen.seqs"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["Filter.seqs"];
  3 -->|fasta_out| 4;
  5["Unique.seqs"];
  4 -->|filteredfasta| 5;
  3 -->|count_out| 5;
  6["Pre.cluster"];
  5 -->|out_fasta| 6;
  5 -->|out_count| 6;
  7["Summary.seqs"];
  6 -->|count_out| 7;
  6 -->|fasta_out| 7;
  a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d["Output\nSummary.seqs on input dataset(s): summary"];
  7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;
  style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;
  8["Chimera.vsearch"];
  6 -->|fasta_out| 8;
  6 -->|count_out| 8;
  9["Remove.seqs"];
  8 -->|out_accnos| 9;
  8 -->|out_count| 9;
  6 -->|fasta_out| 9;
  10["Summary.seqs"];
  9 -->|count_out| 10;
  9 -->|fasta_out| 10;

Inputs

Input Label
Input dataset Aligned Sequences
Input dataset Count Table

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 Summary.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1 Screen.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0 Filter.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0 Unique.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0 Pre.cluster
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 Summary.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1 Chimera.vsearch
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0 Remove.seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 Summary.seqs

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows