Genome Assembly of MRSA using Illumina MiSeq Data

assembly-mrsa-illumina/main-workflow

Author(s)
Bazante Sanders, Bérénice Batut
Version
2
Last updated
Jan 23, 2024
License
MIT
Tags
assembly
microgalaxy

Features
Tutorial
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00018
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 Dataset\nDRR187559_2"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nDRR187559_1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["fastp"];
  1 -->|output| 3;
  0 -->|output| 3;
  5a176468-21e8-4891-80d4-476ebc675ff9["Output\nfastp_json"];
  3 --> 5a176468-21e8-4891-80d4-476ebc675ff9;
  style 5a176468-21e8-4891-80d4-476ebc675ff9 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  5["Shovill"];
  3 -->|out1| 5;
  3 -->|out2| 5;
  16fc6bdf-81a8-463e-b4cd-28c2ec1ce898["Output\nshovill_log"];
  5 --> 16fc6bdf-81a8-463e-b4cd-28c2ec1ce898;
  style 16fc6bdf-81a8-463e-b4cd-28c2ec1ce898 stroke:#2c3143,stroke-width:4px;
  6["Quast"];
  5 -->|contigs| 6;
  59685e1d-e10d-469b-9c7a-317f6685680a["Output\nquast_output"];
  6 --> 59685e1d-e10d-469b-9c7a-317f6685680a;
  style 59685e1d-e10d-469b-9c7a-317f6685680a stroke:#2c3143,stroke-width:4px;
  7["Bandage Image"];
  5 -->|contigs_graph| 7;
  8["Bandage Info"];
  5 -->|contigs_graph| 8;
  169b4956-06bb-4810-bfd1-e0ddcdbcd9e6["Output\nbandage_info_output"];
  8 --> 169b4956-06bb-4810-bfd1-e0ddcdbcd9e6;
  style 169b4956-06bb-4810-bfd1-e0ddcdbcd9e6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
DRR187559_2 DRR187559_2
DRR187559_1 DRR187559_1

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 fastp
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 Shovill
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 Quast
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2 Bandage Info

Tools

Tool Links
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/bandage/bandage_info/2022.09+galaxy2 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/quast/quast/5.2.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 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
7 597f8ce95 2024-01-23 13:57:43 Add Bazante's ORCID
6 03e429090 2024-01-23 10:04:17 Fix workflows
5 c88bcbb6f 2024-01-19 15:28:57 Add license and creator to workflows
4 5fbcc03b0 2024-01-12 15:08:32 Update the MRSA short-read assembly tutorial
3 31848c0ae 2021-01-07 17:16:22 fix linting issues
2 9c83730d5 2021-01-07 16:50:38 Finish illumina version
1 c1175777f 2020-12-18 12:11:55 Add Illumina version of tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/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