Debruijn Graph Velvet Full and SPAdes Assembly

assembly-debruijn-graph-assembly/debruijn-graph-velvet-full-and-spades-assembly

Author(s)
Tristan Reynolds, Delphine Lariviere
Version
1
Last updated
Jan 7, 2026
License
CC-BY-4.0
Tags
assembly

Features
Tutorial
De Bruijn Graph Assembly
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nmutant_R1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmutant_R2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput Paired Reads Collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["VelvetOptimiser"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["velveth"];
  0 -->|output| 4;
  1 -->|output| 4;
  5["SPAdes"];
  2 -->|output| 5;
  d115d043-065d-4a16-9d4a-7b3d4acb4f3c["Output\nspades_log"];
  5 --> d115d043-065d-4a16-9d4a-7b3d4acb4f3c;
  style d115d043-065d-4a16-9d4a-7b3d4acb4f3c stroke:#2c3143,stroke-width:4px;
  6["Fasta Statistics"];
  3 -->|contigs| 6;
  c88b279a-b710-45e4-a6ed-19203271588e["Output\nfasta_stats_velvet"];
  6 --> c88b279a-b710-45e4-a6ed-19203271588e;
  style c88b279a-b710-45e4-a6ed-19203271588e stroke:#2c3143,stroke-width:4px;
  7["velvetg"];
  4 -->|outfile| 7;
  8["Bandage Image"];
  5 -->|out_ags| 8;
  9["Fasta Statistics"];
  5 -->|out_cn| 9;
  2059b810-d964-40d9-afb9-2341fec8f5b8["Output\nfasta_stats_spades"];
  9 --> 2059b810-d964-40d9-afb9-2341fec8f5b8;
  style 2059b810-d964-40d9-afb9-2341fec8f5b8 stroke:#2c3143,stroke-width:4px;
  10["Bandage Image"];
  7 -->|LastGraph| 10;

Inputs

Input Label
Input dataset mutant_R1.fastq
Input dataset mutant_R2.fastq
Input dataset collection Input Paired Reads Collection

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6 VelvetOptimiser
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/4.2.0+galaxy0 SPAdes
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 Bandage Image
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 Bandage Image

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/4.2.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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
2 cf489e98a 2025-12-18 00:05:51 Updated workflows using velvet
1 ae619cffc 2025-12-18 00:03:52 Rename Debruijn-Graph-Velvet-Full-and-SPAdes-Assembly---EU.ga to Debruijn-Graph-Velvet-Full-and-SPAdes-Assembly.ga

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/workflows/Debruijn-Graph-Velvet-Full-and-SPAdes-Assembly.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