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

assembly-mrsa-nanopore/main-workflow

Author(s)
Bazante Sanders, Bérénice Batut
version Version
1
last_modification Last updated
Mar 4, 2024
license License
MIT
galaxy-tags Tags
Assembly

Features

Tutorial
hands_on Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00019
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nNanopore raw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nIllumina forward raw reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nIllumina reverse raw reads"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Convert compressed file to uncompressed."];
  0 -->|output| 3;
  4["FastQC"];
  0 -->|output| 4;
  5["fastp"];
  1 -->|output| 5;
  2 -->|output| 5;
  6["NanoPlot"];
  3 -->|output1| 6;
  a97e6f33-8182-4a33-86dd-6cfbb83a842d["Output\nnanoplot_before_filtering"];
  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;
  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;
  7["filtlong"];
  5 -->|out1| 7;
  5 -->|out2| 7;
  0 -->|output| 7;
  8["Flye"];
  7 -->|outfile| 8;
  f12e718f-1bd5-490d-bd41-f0747aaa41a6["Output\nflye_assembly_info"];
  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;
  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;
  9["NanoPlot"];
  7 -->|outfile| 9;
  89524090-f590-434d-89e2-66f0b1a23c7c["Output\nnanoplot_after_filtering"];
  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;
  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;
  10["Bandage Image"];
  8 -->|assembly_gfa| 10;
  11["BWA-MEM2"];
  5 -->|out2| 11;
  8 -->|consensus| 11;
  12["Quast"];
  8 -->|consensus| 12;
  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c["Output\nquast_report_before_polishing"];
  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;
  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;
  13["BWA-MEM2"];
  5 -->|out1| 13;
  8 -->|consensus| 13;
  14["Polypolish"];
  8 -->|consensus| 14;
  13 -->|bam_output| 14;
  11 -->|bam_output| 14;
  15["Quast"];
  14 -->|polished_fasta| 15;
  8 -->|consensus| 15;
  4e465b51-68bf-4203-9a7c-897f46c70277["Output\nquast_report_after_polishing"];
  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;
  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Nanopore raw reads
Input dataset Illumina forward raw reads
Input dataset Illumina reverse raw reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 NanoPlot
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 Flye
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 NanoPlot
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 Quast
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 Quast

Tools

Tool Links
CONVERTER_bz2_to_uncompressed
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 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/bwa_mem2/bwa_mem2/2.2.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 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 galaxy-upload 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 96393a7fc 2024-02-28 15:52:06 Add MRSA Nanopore assembly tutorial to AMR learning pathway

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