Racon polish with long reads, x4 - upgraded

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nAssembly to be polished"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nlong reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nminimap setting for long reads "];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["Minimap2: map long reads to assembly"];
  2 -->|output| 3;
  1 -->|output| 3;
  0 -->|output| 3;
  4["Racon: polish 1"];
  0 -->|output| 4;
  3 -->|alignment_output| 4;
  1 -->|output| 4;
  5["Minimap2: map long reads to polished assembly 1"];
  2 -->|output| 5;
  1 -->|output| 5;
  4 -->|consensus| 5;
  6["Racon: polish 2"];
  4 -->|consensus| 6;
  5 -->|alignment_output| 6;
  1 -->|output| 6;
  7["Minimap2: map long reads to polished assembly 2"];
  2 -->|output| 7;
  1 -->|output| 7;
  6 -->|consensus| 7;
  8["Racon: polish 3"];
  6 -->|consensus| 8;
  7 -->|alignment_output| 8;
  1 -->|output| 8;
  9["Minimap2: map long reads to polished assembly 3"];
  2 -->|output| 9;
  1 -->|output| 9;
  8 -->|consensus| 9;
  10["Racon: polish 4"];
  8 -->|consensus| 10;
  9 -->|alignment_output| 10;
  1 -->|output| 10;
  bcf0f03c-5951-46a7-aa38-545aed9bc183["Output\nAssembly polished by long reads using Racon"];
  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;
  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;

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/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.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