Assembly polishing - upgraded

assembly-largegenome/galaxy-workflow-assembly-polishing

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:W00009
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\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["ℹ️ Input Dataset\nIllumina reads R1"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["🛠️ Subworkflow\nRacon polish with long reads, x4 - upgraded"];
  style 4 fill:#edd,stroke:#900,stroke-width:4px;
  0 -->|output| 4;
  1 -->|output| 4;
  2 -->|output| 4;
  5["Medaka polish"];
  4 -->|Assembly polished by long reads using Racon| 5;
  1 -->|output| 5;
  e3136060-bce7-4af3-87c4-9dcbb0d1f531["Output\nAssembly polished by long reads using Medaka"];
  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;
  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;
  6["Fasta statistics after Racon long read polish"];
  4 -->|Assembly polished by long reads using Racon| 6;
  7["Fasta statistics after Medaka polish"];
  5 -->|out_consensus| 7;
  8["🛠️ Subworkflow\nRacon polish with Illumina reads R1 only, x2 - upgraded"];
  style 8 fill:#edd,stroke:#900,stroke-width:4px;
  5 -->|out_consensus| 8;
  3 -->|output| 8;
  9["Fasta statistics after Racon short read polish"];
  8 -->|Assembly polished by short reads using Racon| 9;

Inputs

Input Label
Input dataset Assembly to be polished
Input dataset long reads
Input parameter minimap setting (for long reads)
Input dataset Illumina reads R1

Outputs

From Output Label
Input parameter minimap setting (for long reads)
Racon polish with long reads, x4 - upgraded
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1 medaka consensus pipeline Medaka polish

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/fasta_stats/fasta-stats/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+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 091a0834c 2024-05-07 09:31:18 Update Galaxy-Workflow-Assembly_polishing.ga
4 e8ddbcdd5 2024-05-01 04:32:16 new versions of workflows
3 f294a05b5 2024-05-01 04:20:20 Rename Galaxy-Workflow-Assembly_polishing.ga to Galaxy-Workflow-Assembly_polishing_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-Assembly_polishing.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