Genome Assembly Quality Control

assembly-assembly-quality-control/main-workflow

Author(s)
Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier, Laura Leroi
Version
1
Last updated
Aug 26, 2022
License
GPL-3.0-or-later
Tags
assembly

Features
Tutorial
Genome Assembly Quality Control
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00001
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\nGCA_000146045.2_genomic.fna"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nScerevisiae-INSC1019.flye.30x.fa"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nScerevisiae-INSC1019.hifiasm.30x.fa"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSRR13577847_subreads.30x.fastq.gz"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Busco"];
  0 -->|output| 4;
  5["Busco"];
  1 -->|output| 5;
  6["Quast"];
  0 -->|output| 6;
  1 -->|output| 6;
  2 -->|output| 6;
  7["Busco"];
  2 -->|output| 7;
  8["Chromeister"];
  0 -->|output| 8;
  2 -->|output| 8;
  9["Meryl"];
  3 -->|output| 9;
  10["Merqury"];
  0 -->|output| 10;
  9 -->|read_db| 10;
  11["Merqury"];
  1 -->|output| 11;
  9 -->|read_db| 11;
  12["Merqury"];
  2 -->|output| 12;
  9 -->|read_db| 12;

Inputs

Input Label
Input dataset GCA_000146045.2_genomic.fna
Input dataset Scerevisiae-INSC1019.flye.30x.fa
Input dataset Scerevisiae-INSC1019.hifiasm.30x.fa
Input dataset SRR13577847_subreads.30x.fastq.gz

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+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
1 9e51f44fe 2022-08-26 14:11:00 Genome assembly quality control (#3120)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/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