Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nRaw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nheader"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Sort collection"];
  0 -->|output| 2;
  3["dada2: filterAndTrim"];
  2 -->|output| 3;
  4["dada2: plotQualityProfile"];
  2 -->|output| 4;
  5["Unzip collection"];
  3 -->|paired_output| 5;
  6["dada2: plotQualityProfile"];
  3 -->|paired_output| 6;
  7["dada2: learnErrors"];
  5 -->|forward| 7;
  8["dada2: learnErrors"];
  5 -->|reverse| 8;
  9["dada2: dada"];
  5 -->|forward| 9;
  7 -->|errors| 9;
  10["dada2: dada"];
  5 -->|reverse| 10;
  8 -->|errors| 10;
  11["dada2: mergePairs"];
  9 -->|data_collection| 11;
  10 -->|data_collection| 11;
  5 -->|forward| 11;
  5 -->|reverse| 11;
  12["Extract element identifiers"];
  11 -->|merged| 12;
  13["dada2: makeSequenceTable"];
  11 -->|merged| 13;
  3fd25979-39df-4698-bad1-aabfccbb7bd2["Output\nsequence_table"];
  13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;
  style 3fd25979-39df-4698-bad1-aabfccbb7bd2 stroke:#2c3143,stroke-width:4px;
  14["Replace Text"];
  12 -->|output| 14;
  15["dada2: removeBimeraDenovo"];
  13 -->|stable| 15;
  16["Select first"];
  14 -->|outfile| 16;
  17["dada2: sequence counts"];
  3 -->|outtab| 17;
  9 -->|data_collection| 17;
  10 -->|data_collection| 17;
  11 -->|merged| 17;
  15 -->|stable_sequencetable| 17;
  c758f861-44bc-4208-b1f7-1f5106cb678e["Output\nsequence_counts"];
  17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;
  style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;
  18["dada2: assignTaxonomy and addSpecies"];
  15 -->|stable_sequencetable| 18;
  904fe0a2-8329-45ca-8493-fc688fb216c3["Output\ntaxons"];
  18 --> 904fe0a2-8329-45ca-8493-fc688fb216c3;
  style 904fe0a2-8329-45ca-8493-fc688fb216c3 stroke:#2c3143,stroke-width:4px;
  19["Compute"];
  16 -->|outfile| 19;
  20["Replace Text"];
  19 -->|out_file1| 20;
  21["Concatenate datasets"];
  1 -->|output| 21;
  20 -->|outfile| 21;
  5479d320-3e82-47a9-a92b-6ed5959459cf["Output\nmetada_table"];
  21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;
  style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;
  22["Create phyloseq object"];
  21 -->|out_file1| 22;
  15 -->|stable_sequencetable| 22;
  18 -->|output| 22;

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/dada-16S/workflows/workflow.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