Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]
microbiome-mothur-miseq-sop-short/workflow2-data-cleaning
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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
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/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