Metagenomic Binning

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Australia
• Galaxy Main
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nTrimmed reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nRead length CONCOCT"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Collection\nAssemblies"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nEnvironment for the built-in model SemiBin"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["CONCOCT: Cut up contigs"];
  2 -->|output| 4;
  5["Bowtie2"];
  0 -->|output| 5;
  2 -->|output| 5;
  6["Samtools sort"];
  5 -->|output| 6;
  7["CONCOCT: Generate the input coverage table"];
  4 -->|output_bed| 7;
  6 -->|output1| 7;
  8["Calculate contig depths"];
  6 -->|output1| 8;
  9["SemiBin"];
  3 -->|output| 9;
  6 -->|output1| 9;
  2 -->|output| 9;
  10["CONCOCT"];
  1 -->|output| 10;
  4 -->|output_fasta| 10;
  7 -->|output| 10;
  11["MetaBAT2"];
  8 -->|outputDepth| 11;
  2 -->|output| 11;
  12["MaxBin2"];
  8 -->|outputDepth| 12;
  2 -->|output| 12;
  13["Converts genome bins in fasta format"];
  9 -->|output_bins| 13;
  14["CONCOCT: Merge cut clusters"];
  10 -->|output_clustering| 14;
  15["Converts genome bins in fasta format"];
  11 -->|bins| 15;
  16["Converts genome bins in fasta format"];
  12 -->|bins| 16;
  17["CONCOCT: Extract a fasta file"];
  14 -->|output| 17;
  2 -->|output| 17;
  18["Converts genome bins in fasta format"];
  17 -->|bins| 18;
  19["Build list"];
  18 -->|contigs2bin| 19;
  15 -->|contigs2bin| 19;
  16 -->|contigs2bin| 19;
  13 -->|contigs2bin| 19;
  20["Binette"];
  19 -->|output| 20;
  2 -->|output| 20;

Inputs

Outputs

Tools

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity 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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-binning/workflows/Metagenomic-Binning.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