Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nNanopore raw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput Paired End Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["Convert compressed file to uncompressed."];
  0 -->|output| 3;
  4["fastp"];
  1 -->|output| 4;
  f172ab83-f297-40b3-adc0-beb1dbec99ab["Output\nreport_json"];
  4 --> f172ab83-f297-40b3-adc0-beb1dbec99ab;
  style f172ab83-f297-40b3-adc0-beb1dbec99ab stroke:#2c3143,stroke-width:4px;
  5["NanoPlot"];
  3 -->|output1| 5;
  a97e6f33-8182-4a33-86dd-6cfbb83a842d["Output\nnanoplot_before_filtering"];
  5 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;
  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;
  6["Flatten collection"];
  4 -->|output_paired_coll| 6;
  7["Extract Forward Reads"];
  6 -->|output| 7;
  8["Extract Reverse Reads"];
  6 -->|output| 8;
  9["filtlong"];
  7 -->|output| 9;
  8 -->|output| 9;
  0 -->|output| 9;
  10["NanoPlot"];
  9 -->|outfile| 10;
  89524090-f590-434d-89e2-66f0b1a23c7c["Output\nnanoplot_after_filtering"];
  10 --> 89524090-f590-434d-89e2-66f0b1a23c7c;
  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;
  11["Flye"];
  9 -->|outfile| 11;
  f12e718f-1bd5-490d-bd41-f0747aaa41a6["Output\nflye_assembly_info"];
  11 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;
  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;
  12["BWA-MEM2"];
  7 -->|output| 12;
  11 -->|consensus| 12;
  13["Quast"];
  11 -->|consensus| 13;
  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c["Output\nquast_report_before_polishing"];
  13 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;
  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;
  14["Bandage Image"];
  11 -->|assembly_gfa| 14;
  15["BWA-MEM2"];
  8 -->|output| 15;
  11 -->|consensus| 15;
  16["Polypolish"];
  11 -->|consensus| 16;
  12 -->|bam_output| 16;
  15 -->|bam_output| 16;
  17["Quast"];
  11 -->|consensus| 17;
  16 -->|polished_fasta| 17;
  4e465b51-68bf-4203-9a7c-897f46c70277["Output\nquast_report_after_polishing"];
  17 --> 4e465b51-68bf-4203-9a7c-897f46c70277;
  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;

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/assembly/tutorials/mrsa-nanopore/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