Assembly of metagenomic sequencing data

microbiome-metagenomics-assembly/metagenomics-assembly-tutorial-workflow

Author(s)
Polina Polunina, Bérénice Batut
Version
2
Last updated
Jun 16, 2025
License
MIT
Tags
microbiome

Features
Tutorial
Assembly of metagenomic sequencing data
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00125
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 Collection\nQC controlled reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["metaSPAdes"];
  0 -->|output| 1;
  ba8ef041-cea5-479a-8aab-38b3d6f0af60["Output\nout_ag"];
  1 --> ba8ef041-cea5-479a-8aab-38b3d6f0af60;
  style ba8ef041-cea5-479a-8aab-38b3d6f0af60 stroke:#2c3143,stroke-width:4px;
  c3b9a234-94d2-4579-8eba-895e7e49e129["Output\nout_ags"];
  1 --> c3b9a234-94d2-4579-8eba-895e7e49e129;
  style c3b9a234-94d2-4579-8eba-895e7e49e129 stroke:#2c3143,stroke-width:4px;
  2["MEGAHIT"];
  0 -->|output| 2;
  759ce084-a80b-4a04-b74e-6e387357e25a["Output\noutput"];
  2 --> 759ce084-a80b-4a04-b74e-6e387357e25a;
  style 759ce084-a80b-4a04-b74e-6e387357e25a stroke:#2c3143,stroke-width:4px;
  3["Bowtie2"];
  0 -->|output| 3;
  2 -->|output| 3;
  95b806c7-53ee-4a78-8e24-a5794c9c220a["Output\nmapping_stats"];
  3 --> 95b806c7-53ee-4a78-8e24-a5794c9c220a;
  style 95b806c7-53ee-4a78-8e24-a5794c9c220a stroke:#2c3143,stroke-width:4px;
  4["CoverM contig"];
  0 -->|output| 4;
  2 -->|output| 4;
  51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5["Output\noutput"];
  4 --> 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5;
  style 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5 stroke:#2c3143,stroke-width:4px;
  5["Quast"];
  2 -->|output| 5;
  0 -->|output| 5;
  5553b6a6-863d-4846-944f-7ed609a3734a["Output\nreport_html_meta"];
  5 --> 5553b6a6-863d-4846-944f-7ed609a3734a;
  style 5553b6a6-863d-4846-944f-7ed609a3734a stroke:#2c3143,stroke-width:4px;
  6["megahit contig2fastg"];
  2 -->|output| 6;
  7["Bandage Image"];
  6 -->|fastg| 7;
  63861d0b-e0a6-4604-bd09-1b0f7ee9d54b["Output\noutfile"];
  7 --> 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b;
  style 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b stroke:#2c3143,stroke-width:4px;
  8["Bandage Info"];
  6 -->|fastg| 8;
  9["Column join"];
  8 -->|outfile| 9;
  c882d313-5084-40d4-8c97-9552fb7b35ad["Output\ntabular_output"];
  9 --> c882d313-5084-40d4-8c97-9552fb7b35ad;
  style c882d313-5084-40d4-8c97-9552fb7b35ad stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection QC controlled reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0 metaSPAdes
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 MEGAHIT
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 Bowtie2
toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 CoverM contig
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 Quast
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4 Bandage Image
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 Column join

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+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
  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 65e24d135 2025-06-12 09:54:14 Update metagenomics assembly tutorial
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_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