Workflow to detect SNV from Illumina sequenced baculovirus isolates

Run Workflow in Galaxy

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

flowchart TD
  0["Download reference genome in FASTA format from NCBI"];
  1["Paired dataset collection in FASTQ format downloaded from NCBI SRA"];
  2["Collapse Genbank file"];
  0 -->|output| 2;
  3["Trim Galore!"];
  1 -->|list_paired| 3;
  4["Rename reference genome sequence header"];
  2 -->|output| 4;
  5["Map with BWA-MEM"];
  3 -->|trimmed_reads_paired_collection| 5;
  4 -->|outfile| 5;
  6["bcftools mpileup"];
  5 -->|bam_output| 6;
  4 -->|outfile| 6;
  7["bcftools call"];
  6 -->|output_file| 7;
  d8a45d4f-c8e4-40da-ba84-7ec13aa8ca4d["Output\nbcftools_call_output"];
  7 --> d8a45d4f-c8e4-40da-ba84-7ec13aa8ca4d;
  style d8a45d4f-c8e4-40da-ba84-7ec13aa8ca4d stroke:#2c3143,stroke-width:4px;
  8["VCF Transformation"];
  7 -->|output_file| 8;
  9["Relative allele frequency calculation"];
  8 -->|out_file1| 9;
  10["Replace Text"];
  9 -->|outfile| 10;
  186d4e5c-fceb-4031-b569-d84dbcd1c156["Output\nvcf_table"];
  10 --> 186d4e5c-fceb-4031-b569-d84dbcd1c156;
  style 186d4e5c-fceb-4031-b569-d84dbcd1c156 stroke:#2c3143,stroke-width:4px;
  11["Reduce dataset to ALT1"];
  10 -->|outfile| 11;
  7ebeb330-a4df-4027-b636-daa0e5e39938["Output\nvcf_table_ALT1"];
  11 --> 7ebeb330-a4df-4027-b636-daa0e5e39938;
  style 7ebeb330-a4df-4027-b636-daa0e5e39938 stroke:#2c3143,stroke-width:4px;
  12["SNV plot"];
  11 -->|out_file1| 12;
  13["SNV specificity calculation"];
  11 -->|out_file1| 13;
  b2f9dabd-7bbf-4b96-a351-78a2b2552586["Output\nvcf_table_ALT1_specificity"];
  13 --> b2f9dabd-7bbf-4b96-a351-78a2b2552586;
  style b2f9dabd-7bbf-4b96-a351-78a2b2552586 stroke:#2c3143,stroke-width:4px;
  14["Filter"];
  13 -->|outfile| 14;
  15["Filter"];
  13 -->|outfile| 15;
  16["Filter"];
  13 -->|outfile| 16;
  17["ggplot2 V15 dotplot "];
  14 -->|out_file1| 17;
  18["ggplot2 CpGV-S dotplot"];
  15 -->|out_file1| 18;
  19["ggplot2 CpGV-E2 dotplot"];
  16 -->|out_file1| 19;

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/variant-analysis/tutorials/baculovirus-isolate-variation/workflows/Workflow-to-detect-SNV-from-Illumina-sequenced-baculovirus-isolates.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