Genome Assembly using PacBio data

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nPacBio reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Flye"];
  0 -->|output| 2;
  d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a["Output\nFlye on input dataset(s): assembly info"];
  2 --> d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a;
  style d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a stroke:#2c3143,stroke-width:4px;
  c8f96c22-e06e-4fec-bbfa-d993b7b103eb["Output\nFlye on input dataset(s): consensus"];
  2 --> c8f96c22-e06e-4fec-bbfa-d993b7b103eb;
  style c8f96c22-e06e-4fec-bbfa-d993b7b103eb stroke:#2c3143,stroke-width:4px;
  a288fb93-5aa5-4231-89e4-958c57106978["Output\nFlye on input dataset(s): graphical fragment assembly"];
  2 --> a288fb93-5aa5-4231-89e4-958c57106978;
  style a288fb93-5aa5-4231-89e4-958c57106978 stroke:#2c3143,stroke-width:4px;
  0e064181-5cd4-42c8-98f9-fe417303956c["Output\nFlye on input dataset(s): assembly graph"];
  2 --> 0e064181-5cd4-42c8-98f9-fe417303956c;
  style 0e064181-5cd4-42c8-98f9-fe417303956c stroke:#2c3143,stroke-width:4px;
  3["Fasta Statistics"];
  1 -->|output| 3;
  4["Busco"];
  1 -->|output| 4;
  5["Fasta Statistics"];
  2 -->|consensus| 5;
  6["Quast"];
  1 -->|output| 6;
  2 -->|consensus| 6;
  bea191cb-f88d-4103-b8fa-b3683d77cc93["Output\nQuast on input dataset(s):  HTML report"];
  6 --> bea191cb-f88d-4103-b8fa-b3683d77cc93;
  style bea191cb-f88d-4103-b8fa-b3683d77cc93 stroke:#2c3143,stroke-width:4px;
  7["Busco"];
  2 -->|consensus| 7;

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/flye-assembly/workflows/main_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