Genome Assembly using PacBio data

assembly-flye-assembly/main-workflow

Author(s)
Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier
Version
1
Last updated
Nov 29, 2021
License
GPL-3.0-or-later
Tags
assembly

Features
Tutorial
Genome assembly using PacBio data
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00007
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset PacBio reads
Input dataset Reference genome

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0 Flye
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3 Quast
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 Busco

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3 View in ToolShed

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

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

Version History

Version Commit Time Comments
4 6e12dcba4 2021-11-29 09:11:49 update quast
3 a086911d0 2021-11-26 14:56:18 update workflow + minor changes
2 b8606bace 2021-11-26 12:58:23 flye-assembly workflow modified with new tools versions
1 e817e8cfd 2021-10-26 15:11:00 added flye assembly tutorial

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