Racon polish with Illumina reads (R1 only), x2 - upgraded

assembly-largegenome/galaxy-workflow-racon-polish-with-illumina-reads-x2

Author(s)
Anna Syme
Version
2
Last updated
May 8, 2024
License
GPL-3.0-or-later
Tags
LG-WF
GTN

Features
Tutorial
Large genome assembly and polishing
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00014
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nAssembly to be polished"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nIllumina reads, R1, in fastq.gz format"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Minimap2 round 1: map reads to assembly"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Racon round 1: polish assembly"];
  0 -->|output| 3;
  2 -->|alignment_output| 3;
  1 -->|output| 3;
  4["Minimap2 round 2: map reads to assembly"];
  1 -->|output| 4;
  3 -->|consensus| 4;
  5["Racon round 2: polish assembly"];
  3 -->|consensus| 5;
  4 -->|alignment_output| 5;
  1 -->|output| 5;
  594819c3-668e-4575-b9a6-4459ffacf952["Output\nAssembly polished by short reads using Racon"];
  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;
  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Assembly to be polished
Input dataset Illumina reads, R1, in fastq.gz format

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1 Racon Racon round 2: polish assembly

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 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
5 3be0312ca 2024-05-07 09:33:23 Update Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga
4 e8ddbcdd5 2024-05-01 04:32:16 new versions of workflows
3 7d222309f 2024-05-01 04:21:33 Rename Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga to Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2_old.ga
2 62e77944b 2023-02-17 09:53:23 add/complete creator info on workflows
1 9fcb3aeec 2022-10-07 06:24:16 large genome tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.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