Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nDRR187559_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nDRR187559_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC forward"];
  0 -->|output| 2;
  d3aed14e-51b8-40b0-9d6d-548fff2ab63a["Output\nFastQC text_file (forward)"];
  2 --> d3aed14e-51b8-40b0-9d6d-548fff2ab63a;
  style d3aed14e-51b8-40b0-9d6d-548fff2ab63a stroke:#2c3143,stroke-width:4px;
  6c927338-7e02-4599-a01d-014a35a529e8["Output\nFastQC html_file (forward)"];
  2 --> 6c927338-7e02-4599-a01d-014a35a529e8;
  style 6c927338-7e02-4599-a01d-014a35a529e8 stroke:#2c3143,stroke-width:4px;
  3["FastQC reverse"];
  1 -->|output| 3;
  30d76c09-809d-4415-a1e6-f244cfc34065["Output\nFastQC html_file (reverse)"];
  3 --> 30d76c09-809d-4415-a1e6-f244cfc34065;
  style 30d76c09-809d-4415-a1e6-f244cfc34065 stroke:#2c3143,stroke-width:4px;
  bbafb072-8b12-4908-ae0f-10cc7f9086d3["Output\nFastQC text_file (reverse)"];
  3 --> bbafb072-8b12-4908-ae0f-10cc7f9086d3;
  style bbafb072-8b12-4908-ae0f-10cc7f9086d3 stroke:#2c3143,stroke-width:4px;
  4["fastp"];
  0 -->|output| 4;
  1 -->|output| 4;
  1a089ca0-445a-4322-b74f-60c7aefc7cd8["Output\nfastp report_html"];
  4 --> 1a089ca0-445a-4322-b74f-60c7aefc7cd8;
  style 1a089ca0-445a-4322-b74f-60c7aefc7cd8 stroke:#2c3143,stroke-width:4px;
  b634addf-dcb8-43e6-8016-341de7eb5b87["Output\nDRR187559_filtered_"];
  4 --> b634addf-dcb8-43e6-8016-341de7eb5b87;
  style b634addf-dcb8-43e6-8016-341de7eb5b87 stroke:#2c3143,stroke-width:4px;
  0a57afa4-e75e-470d-ad7b-13e567ce54a3["Output\nDRR187559_filtered_1"];
  4 --> 0a57afa4-e75e-470d-ad7b-13e567ce54a3;
  style 0a57afa4-e75e-470d-ad7b-13e567ce54a3 stroke:#2c3143,stroke-width:4px;
  bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50["Output\nfastp_json"];
  4 --> bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50;
  style bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50 stroke:#2c3143,stroke-width:4px;
  5["Kraken2"];
  4 -->|out1| 5;
  4 -->|out2| 5;
  54b85a53-72ee-4b73-b186-7fd55e8aab9b["Output\nkraken_report_tabular"];
  5 --> 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"];
  5 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;
  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;
  6["Bracken"];
  5 -->|report_output| 6;
  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8["Output\nbracken_kraken_report"];
  6 --> 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"];
  6 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;
  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;
  7["Recentrifuge"];
  5 -->|output| 7;
  bd947a1d-0443-465f-8658-5d76d9ce69f8["Output\nrecentrifuge_report_html"];
  7 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;
  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;
  c7457acb-41bc-4191-b3fb-6716e15fbe57["Output\nrecentrifuge_data_tabular"];
  7 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;
  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;
  b5694f2d-c8cd-4460-bfff-74fd0792ecb3["Output\nrecentrifuge_stats_tabular"];
  7 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;
  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;
  94f6ff07-0e06-47ad-88f8-a058d0808537["Output\nrecentrifuge_logfile"];
  7 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;
  style 94f6ff07-0e06-47ad-88f8-a058d0808537 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

• 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:

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