Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput Paired Reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Falco"];
  0 -->|output| 1;
  64d295db-1808-40e6-afd2-af20f4e178f6["Output\nFalco text_file (forward)"];
  1 --> 64d295db-1808-40e6-afd2-af20f4e178f6;
  style 64d295db-1808-40e6-afd2-af20f4e178f6 stroke:#2c3143,stroke-width:4px;
  13fee5d7-3fc7-44f9-81a1-ed84daa2da03["Output\nFalco html_file (forward)"];
  1 --> 13fee5d7-3fc7-44f9-81a1-ed84daa2da03;
  style 13fee5d7-3fc7-44f9-81a1-ed84daa2da03 stroke:#2c3143,stroke-width:4px;
  2["fastp"];
  0 -->|output| 2;
  bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50["Output\nfastp_json"];
  2 --> bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50;
  style bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50 stroke:#2c3143,stroke-width:4px;
  1a089ca0-445a-4322-b74f-60c7aefc7cd8["Output\nfastp report_html"];
  2 --> 1a089ca0-445a-4322-b74f-60c7aefc7cd8;
  style 1a089ca0-445a-4322-b74f-60c7aefc7cd8 stroke:#2c3143,stroke-width:4px;
  3["Kraken2"];
  2 -->|output_paired_coll| 3;
  54b85a53-72ee-4b73-b186-7fd55e8aab9b["Output\nkraken_report_tabular"];
  3 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;
  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;
  a408a644-58cd-4f5e-af25-15b5ea63aa76["Output\nkraken_report_reads"];
  3 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;
  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;
  4["Bracken"];
  3 -->|report_output| 4;
  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8["Output\nbracken_kraken_report"];
  4 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;
  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;
  ae6c6464-f5f5-4e5b-b616-d38166fc0133["Output\nbracken_report_tsv"];
  4 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;
  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;
  5["Recentrifuge"];
  3 -->|output| 5;
  c7457acb-41bc-4191-b3fb-6716e15fbe57["Output\nrecentrifuge_data_tabular"];
  5 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;
  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;
  bd947a1d-0443-465f-8658-5d76d9ce69f8["Output\nrecentrifuge_report_html"];
  5 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;
  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;
  b5694f2d-c8cd-4460-bfff-74fd0792ecb3["Output\nrecentrifuge_stats_tabular"];
  5 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;
  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 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/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality-and-contamination-control-in-bacterial-isolate-using-Illumina-MiSeq-Data.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