Your First Analysis

Variant Calling from Sequencing Data

This walkthrough demonstrates how to perform pathogen surveillance analysis using the measles virus example from the featured analysis.

Step 1: Select Your Organism

  1. From the BRC Analytics homepage, navigate to "Organisms"
  2. Use the search or browse function to find your organism of interest
    • Example: Search for "Measles morbillivirus"
  3. Click on the organism to view available assemblies

Step 2: Choose a Reference Assembly

  1. Review the available genome assemblies from NCBI.
  2. For Measles morbillivirus, there is a single RefSeq assembly (GCF_000854845.1). Select that assembly and review the metadata (assembly level, genome size, annotations).
  3. Click "View", select "UCSC Genome Browser" to explore the genome visually (optional).
  4. Click "Analyze" to load the workflow selection screen.

Step 3: Select a Workflow

The workflow page shows a “Custom Analysis” option plus a Select a workflow section with categories (Variant calling, Transcriptomics, Regulation, Consensus sequences, and additional “coming soon” groups).

  1. In Select a workflow, choose the Variant calling category.
  2. Pick the "Variant calling and consensus construction from paired end short read data of non-segmented viral genomes" workflow.

Step 4: Get Your Data

The workflow form will automatically select the reference FASTA and/or compatible indices based on the assembly you chose. You will still pick the annotation set— for this measles example choose “NCBI Gene” (the only option provided).

BRC Analytics offers three ways to supply sequencing reads:

  1. Browse public reads available via ENA (auto-filtered to match the workflow’s layout/strategy, but you can adjust filters).
  2. Enter known accessions (paste BioProject IDs or individual SRRs).
  3. Upload your own FASTQ files directly into Galaxy.

For this walkthrough, use the same public surveillance data highlighted in the featured analysis:

  1. Click "Browse [N] Sequences".
  2. Search for each of the following BioProjects and add their paired-end runs:
    • PRJNA1145141 (Romania outbreak, 124 samples)
    • PRJNA1017431 (Canada surveillance, 61 samples)
    • PRJNA869081 (Operation Allies Welcome dataset, 42 samples)
  3. Keep the default workflow filters (paired-end, whole-genome sequencing) so results stay compatible.
  4. Select the desired runs and continue; the platform will queue downloads automatically.

Step 5: Launch in Galaxy and Monitor the Run

  1. Click "Launch in Galaxy"; you will land in your most recently active Galaxy history (create a new history if you want to keep this analysis separate).
  2. In Galaxy, review the workflow form before starting the run. Common parameters include:
    • Base quality threshold - Minimum quality score for variant calling (typically 20-30)
    • Allele frequency threshold - Minimum frequency to call a variant (e.g., 0.05 for 5%)
    • Read depth - Minimum coverage required
    • Trimming options - Adapter removal and quality trimming settings
  3. When ready, click "Run workflow" and monitor progress in the Galaxy history panel (right side). Each dataset tile shows status; expand tiles to inspect logs if needed.

For the measles virus variant workflow:

  1. Review default parameters (optimized for viral genomes)
  2. Adjust thresholds if desired. The default settings are appropriate for this analysis.
  3. The workflow will automatically:
    • Trim adapter sequences
    • Map reads to the reference genome
    • Call variants with iVar
    • Generate consensus sequences
    • Annotate variants with SnpEff
    • Produce quality control reports with MultiQC

Step 6: View Results

Analysis outputs include:

Primary Results:

  • Trimmed reads - Quality-filtered sequencing data
  • BAM files - Mapped and aligned reads
  • VCF files - Annotated variant calls with summary tables
  • Consensus FASTA - Per-sample consensus sequences
  • QC reports - Integrated quality metrics

Accessing results:

  1. Click on any dataset in your history to expand details
  2. Click the eye icon to view data
  3. Click the download icon to save locally
  4. Click the info icon for provenance and parameters

Next Steps

Beginner Path

  1. Complete the Getting Started guides
  2. Try the Galaxy 101 tutorial
  3. Run the measles virus featured analysis to see how the workflow outputs feed into downstream evolutionary interpretation
  4. Find your organism and assembly of interest in the Organisms explorer and review the available metadata
  5. Explore the workflow inputs available for that assembly and use the Custom analysis route to inspect them directly in Galaxy

Intermediate Path

  1. Explore additional features in Common Workflows
  2. Use JupyterLite for custom analyses
  3. Upload your own data as Galaxy collections for batch runs
  4. Visualize results via UCSC Genome Browser integration
  5. Share or re-run workflows using the Galaxy workflow sharing tips

Advanced Path

  1. Develop custom workflows using the Custom analysis route and contribute to the Intergalactic Workflow Commission
  2. Integrate multiple data types with the multi-omics GSEA tutorial
  3. Fork and refine workflows in the Galaxy workflow editor to capture advanced logic without scripting
  4. Publish reproducible research by sharing histories or Galaxy Pages via the history sharing guide