Training: 16S rRNA Sequencing With Mothur: Main Tutorial

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Main
• Galaxy France
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nInput FASTQ pairs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsilva.v4.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Count.seqs"];
  8 -->|groups_out| 10;
  9 -->|out_names| 10;
  11["Align.seqs"];
  1 -->|output| 11;
  9 -->|out_fasta| 11;
  12["Summary.seqs"];
  10 -->|seq_count| 12;
  11 -->|out_align| 12;
  13["Screen.seqs"];
  10 -->|seq_count| 13;
  11 -->|out_align| 13;
  14["Filter.seqs"];
  13 -->|fasta_out| 14;
  15["Unique.seqs"];
  14 -->|filteredfasta| 15;
  13 -->|count_out| 15;
  16["Pre.cluster"];
  15 -->|out_fasta| 16;
  15 -->|out_count| 16;
  17["Chimera.vsearch"];
  16 -->|fasta_out| 17;
  16 -->|count_out| 17;
  18["Remove.seqs"];
  17 -->|out_accnos| 18;
  17 -->|out_count| 18;
  16 -->|fasta_out| 18;
  19["Classify.seqs"];
  2 -->|output| 19;
  18 -->|count_out| 19;
  18 -->|fasta_out| 19;
  3 -->|output| 19;
  2["ℹ️ Input Dataset\ntrainset9_032012.pds.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Remove.lineage"];
  18 -->|count_out| 20;
  18 -->|fasta_out| 20;
  19 -->|taxonomy_out| 20;
  21["Get.groups"];
  20 -->|fasta_out| 21;
  20 -->|count_out| 21;
  22["Remove.groups"];
  20 -->|fasta_out| 22;
  20 -->|count_out| 22;
  20 -->|taxonomy_out| 22;
  23["Seq.error"];
  4 -->|output| 23;
  21 -->|count_out| 23;
  21 -->|fasta_out| 23;
  24["Dist.seqs"];
  21 -->|fasta_out| 24;
  25["Cluster.split"];
  22 -->|fasta_out| 25;
  22 -->|count_out| 25;
  22 -->|taxonomy_out| 25;
  26["Cluster"];
  21 -->|count_out| 26;
  24 -->|out_dist| 26;
  27["Make.shared"];
  22 -->|count_out| 27;
  25 -->|otulist| 27;
  28["Classify.otu"];
  22 -->|count_out| 28;
  25 -->|otulist| 28;
  22 -->|taxonomy_out| 28;
  29["Make.shared"];
  21 -->|count_out| 29;
  26 -->|otulist| 29;
  3["ℹ️ Input Dataset\ntrainset9_032012.pds.tax"];
  style 3 stroke:#2c3143,stroke-width:4px;
  30["Summary.single"];
  27 -->|shared| 30;
  31["Count.groups"];
  27 -->|shared| 31;
  32["Dist.shared"];
  27 -->|shared| 32;
  33["Rarefaction.single"];
  27 -->|shared| 33;
  34["Sub.sample"];
  27 -->|shared| 34;
  35["Taxonomy-to-Krona"];
  28 -->|taxonomies| 35;
  36["Rarefaction.single"];
  29 -->|shared| 36;
  37["Tree.shared"];
  32 -->|distfiles| 37;
  38["Heatmap.sim"];
  32 -->|distfiles| 38;
  39["Plotting tool"];
  33 -->|rarefactioncurves| 39;
  4["ℹ️ Input Dataset\nHMP_MOCK.v35.fasta"];
  style 4 stroke:#2c3143,stroke-width:4px;
  40["Venn"];
  34 -->|shared_out| 40;
  41["Make.biom"];
  28 -->|taxonomies| 41;
  5 -->|output| 41;
  34 -->|shared_out| 41;
  42["Krona pie chart"];
  35 -->|outputfile| 42;
  43["Newick Display"];
  37 -->|tre| 43;
  5["ℹ️ Input Dataset\nmouse.dpw.metadata"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Make.contigs"];
  0 -->|output| 6;
  7["Summary.seqs"];
  6 -->|fasta| 7;
  8["Screen.seqs"];
  6 -->|fasta| 8;
  6 -->|group| 8;
  9["Unique.seqs"];
  8 -->|fasta_out| 9;

Inputs

Outputs

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.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