Amplicon Tutorial

microbiome-general-tutorial/amplicon

Author(s)

version Version
1
last_modification Last updated
Jan 15, 2024
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
microbiome

Features

Tutorial
hands_on Analyses of metagenomics data - The global picture
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00123
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nSILVA Reference"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnguil Soil Sample"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPampa Soil Sample"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTrainset PDS alignment"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nTrainset PDS taxonomy"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Merge.files"];
  2 -->|output| 5;
  1 -->|output| 5;
  6["Make.group"];
  1 -->|output| 6;
  2 -->|output| 6;
  7["Unique.seqs"];
  5 -->|output| 7;
  8["Count.seqs"];
  6 -->|output| 8;
  7 -->|out_names| 8;
  9["Summary.seqs"];
  8 -->|seq_count| 9;
  7 -->|out_fasta| 9;
  10["Screen.seqs"];
  7 -->|out_fasta| 10;
  8 -->|seq_count| 10;
  11["Align.seqs"];
  0 -->|output| 11;
  10 -->|fasta_out| 11;
  12["Summary.seqs"];
  10 -->|count_out| 12;
  11 -->|out_file| 12;
  13["Screen.seqs"];
  11 -->|out_file| 13;
  10 -->|count_out| 13;
  14["Filter.seqs"];
  13 -->|fasta_out| 14;
  15["Pre.cluster"];
  14 -->|filteredfasta| 15;
  13 -->|count_out| 15;
  16["Classify.seqs"];
  15 -->|count_out| 16;
  3 -->|output| 16;
  15 -->|fasta_out| 16;
  4 -->|output| 16;
  17["Cluster.split"];
  16 -->|taxonomy_out| 17;
  15 -->|fasta_out| 17;
  15 -->|count_out| 17;
  18["Make.shared"];
  15 -->|count_out| 18;
  17 -->|otulist| 18;
  f1552817-71b2-4546-8ed7-02751d4f6b47["Output\nmothur_make_shared_shared"];
  18 --> f1552817-71b2-4546-8ed7-02751d4f6b47;
  style f1552817-71b2-4546-8ed7-02751d4f6b47 stroke:#2c3143,stroke-width:4px;
  19["Classify.otu"];
  15 -->|count_out| 19;
  16 -->|taxonomy_out| 19;
  17 -->|otulist| 19;
  20["Make.biom"];
  18 -->|shared| 20;
  19 -->|taxonomies| 20;
  21["Visualize  with Krona"];
  19 -->|taxonomies| 21;

Inputs

Input Label
Input dataset SILVA Reference
Input dataset Anguil Soil Sample
Input dataset Pampa Soil Sample
Input dataset Trainset PDS alignment
Input dataset Trainset PDS taxonomy

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0 Make.shared

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1 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 galaxy-upload 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/general-tutorial/workflows/amplicon.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