Metabarcoding Dunnart QIIME2 Analysis

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput Paired End Reads Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsilva_138.2_16s_v4_classifier.qza"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ndunnart_metadata.tsv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Cutadapt"];
  0 -->|output| 3;
  4["Flatten collection"];
  3 -->|out_pairs| 4;
  5["Extract element identifiers"];
  4 -->|output| 5;
  6["Regex Find And Replace"];
  5 -->|output| 6;
  7["Paste"];
  5 -->|output| 7;
  6 -->|out_file1| 7;
  8["Relabel identifiers"];
  7 -->|out_file1| 8;
  4 -->|output| 8;
  9["qiime2 tools import"];
  8 -->|output| 9;
  10["qiime2 demux summarize"];
  9 -->|imported_data| 10;
  11["qiime2 dada2 denoise-paired"];
  9 -->|imported_data| 11;
  12["qiime2 feature-table tabulate-seqs"];
  11 -->|representative_sequences| 12;
  13["qiime2 metadata tabulate"];
  11 -->|denoising_stats| 13;
  14["qiime2 feature-table summarize"];
  2 -->|output| 14;
  11 -->|table| 14;
  15["qiime2 feature-classifier classify-sklearn"];
  1 -->|output| 15;
  11 -->|representative_sequences| 15;
  16["qiime2 phylogeny align-to-tree-mafft-fasttree"];
  11 -->|representative_sequences| 16;
  17["qiime2 tools export"];
  15 -->|classification| 17;
  18["qiime2 taxa filter-table"];
  11 -->|table| 18;
  15 -->|classification| 18;
  19["qiime2 metadata tabulate"];
  15 -->|classification| 19;
  20["qiime2 tools export"];
  16 -->|tree| 20;
  e5b70c15-45bb-4e11-88b7-5bc77f792037["Output\nNewickDirectoryFormat"];
  20 --> e5b70c15-45bb-4e11-88b7-5bc77f792037;
  style e5b70c15-45bb-4e11-88b7-5bc77f792037 stroke:#2c3143,stroke-width:4px;
  21["Remove beginning"];
  17 -->|TSVTaxonomyDirectoryFormat| 21;
  8caac6b6-e1f7-471e-88b2-2e3f16a9ce2d["Output\ntaxonomy_noHeader.tsv"];
  21 --> 8caac6b6-e1f7-471e-88b2-2e3f16a9ce2d;
  style 8caac6b6-e1f7-471e-88b2-2e3f16a9ce2d stroke:#2c3143,stroke-width:4px;
  22["qiime2 tools export"];
  18 -->|filtered_table| 22;
  23["qiime2 taxa barplot"];
  2 -->|output| 23;
  15 -->|classification| 23;
  18 -->|filtered_table| 23;
  24["qiime2 feature-table summarize"];
  2 -->|output| 24;
  18 -->|filtered_table| 24;
  25["qiime2 composition ancombc2"];
  2 -->|output| 25;
  18 -->|filtered_table| 25;
  26["qiime2 diversity alpha-rarefaction"];
  2 -->|output| 26;
  16 -->|rooted_tree| 26;
  18 -->|filtered_table| 26;
  27["qiime2 diversity core-metrics-phylogenetic"];
  2 -->|output| 27;
  16 -->|rooted_tree| 27;
  18 -->|filtered_table| 27;
  28["Convert"];
  22 -->|BIOMV210DirFmt| 28;
  29["Build list"];
  10 -->|visualization| 29;
  12 -->|visualization| 29;
  13 -->|visualization| 29;
  19 -->|visualization| 29;
  14 -->|summary| 29;
  23 -->|visualization| 29;
  24 -->|summary| 29;
  30["qiime2 composition ancombc2-visualizer"];
  15 -->|classification| 30;
  25 -->|ancombc2_output| 30;
  31["qiime2 diversity alpha-group-significance"];
  27 -->|observed_features_vector| 31;
  2 -->|output| 31;
  32["qiime2 diversity alpha-group-significance"];
  27 -->|evenness_vector| 32;
  2 -->|output| 32;
  33["qiime2 diversity beta-group-significance"];
  27 -->|unweighted_unifrac_distance_matrix| 33;
  2 -->|output| 33;
  34["Remove beginning"];
  28 -->|output_fp| 34;
  977bd5f4-3a1f-4c5f-ace0-c571b6922e2b["Output\nfeature-table_noHeader.tsv"];
  34 --> 977bd5f4-3a1f-4c5f-ace0-c571b6922e2b;
  style 977bd5f4-3a1f-4c5f-ace0-c571b6922e2b stroke:#2c3143,stroke-width:4px;
  35["Build list"];
  26 -->|visualization| 35;
  30 -->|visualization| 35;
  31 -->|visualization| 35;
  32 -->|visualization| 35;
  33 -->|visualization| 35;
  27 -->|unweighted_unifrac_emperor| 35;
  27 -->|weighted_unifrac_emperor| 35;
  27 -->|jaccard_emperor| 35;
  27 -->|bray_curtis_emperor| 35;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/dunnart_metabarcoding/workflows/Metabarcoding-Dunnart-QIIME2-Analysis.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