Hybrid Genome Assembly Tutorial Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nreference_genome.fasta"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nillumina_reads_1.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nillumina_reads_2.fastq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nnanopore_reads.fastq"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Busco"];
  0 -->|output| 4;
  3f8fa313-700f-4224-b91a-5a633df32e14["Output\nbusco_sum_ref"];
  4 --> 3f8fa313-700f-4224-b91a-5a633df32e14;
  style 3f8fa313-700f-4224-b91a-5a633df32e14 stroke:#2c3143,stroke-width:4px;
  5["Flye"];
  3 -->|output| 5;
  6["Create assemblies with Unicycler"];
  3 -->|output| 6;
  1 -->|output| 6;
  2 -->|output| 6;
  7["Quast"];
  0 -->|output| 7;
  5 -->|consensus| 7;
  17f4e143-98c8-4888-b77d-86d64e6fa21e["Output\nreport_html_raw_assembly"];
  7 --> 17f4e143-98c8-4888-b77d-86d64e6fa21e;
  style 17f4e143-98c8-4888-b77d-86d64e6fa21e stroke:#2c3143,stroke-width:4px;
  8["Busco"];
  5 -->|consensus| 8;
  bafa6bef-63fb-43a4-b967-1b7323278939["Output\nbusco_sum_raw_assembly"];
  8 --> bafa6bef-63fb-43a4-b967-1b7323278939;
  style bafa6bef-63fb-43a4-b967-1b7323278939 stroke:#2c3143,stroke-width:4px;
  9["Map with BWA-MEM"];
  1 -->|output| 9;
  2 -->|output| 9;
  5 -->|consensus| 9;
  10["Quast"];
  0 -->|output| 10;
  6 -->|assembly| 10;
  76bb1ad9-8ad0-459e-bccb-af440b7eb614["Output\nreport_html_unicy_assembly"];
  10 --> 76bb1ad9-8ad0-459e-bccb-af440b7eb614;
  style 76bb1ad9-8ad0-459e-bccb-af440b7eb614 stroke:#2c3143,stroke-width:4px;
  11["Busco"];
  6 -->|assembly| 11;
  c26bd17f-6fb2-4a74-b4fe-091c05a90806["Output\nbusco_sum_unicy_assembly"];
  11 --> c26bd17f-6fb2-4a74-b4fe-091c05a90806;
  style c26bd17f-6fb2-4a74-b4fe-091c05a90806 stroke:#2c3143,stroke-width:4px;
  12["pilon"];
  9 -->|bam_output| 12;
  5 -->|consensus| 12;
  13["Quast"];
  0 -->|output| 13;
  12 -->|output_fasta| 13;
  04f75a82-c935-4cde-beb8-b45451f087b8["Output\nreport_html_polish_assembly"];
  13 --> 04f75a82-c935-4cde-beb8-b45451f087b8;
  style 04f75a82-c935-4cde-beb8-b45451f087b8 stroke:#2c3143,stroke-width:4px;
  14["Busco"];
  12 -->|output_fasta| 14;
  318563f3-b5a5-47bd-9a5d-c1d54ce3231c["Output\nbusco_sum_polish_assembly"];
  14 --> 318563f3-b5a5-47bd-9a5d-c1d54ce3231c;
  style 318563f3-b5a5-47bd-9a5d-c1d54ce3231c stroke:#2c3143,stroke-width:4px;
  15["MultiQC"];
  4 -->|busco_sum| 15;
  8 -->|busco_sum| 15;
  11 -->|busco_sum| 15;
  14 -->|busco_sum| 15;
  7 -->|report_tabular| 15;
  10 -->|report_tabular| 15;
  13 -->|report_tabular| 15;
  aeb424b5-39b7-42da-a4fc-b04b9bac8091["Output\nmultiqc_html_report"];
  15 --> aeb424b5-39b7-42da-a4fc-b04b9bac8091;
  style aeb424b5-39b7-42da-a4fc-b04b9bac8091 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/hybrid_denovo_assembly/workflows/Hybrid-Genome-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