Workflows

These workflows are associated with Genome assembly using PacBio data

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.

Genome Assembly using PacBio data
Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier

Last updated Nov 29, 2021

Launch in Tutorial Mode
License: GPL-3.0-or-later
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy France Galaxy Main Galaxy Europe 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;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL