Illumina Variant Calling Pro Workflow
Quickstart Guide
Version 1.0 | Last updated August 23, 2021
  1. Upload data files (FASTQ) or select from the sample data library or history

    • If uploading data, see Uploading Data
    • If using provided sample data, see Getting Sample Data
  2. Upload Reference Transcriptome (FASTA) or select from preloaded options

    • If using a preloaded reference, this is selected when starting the workflow
  3. Format data into collections if not using provided samples

    • See Formatting Collections
  4. Select workflow

    • Select Workflows from the Shared Data tab in the masthead
    • Select either Single-End Illumina Variant Calling or Paired-End Illumina Variant Calling
    • Click the drop down arrow to the right of the workflow name and select Run
  5. Select Input Files and Medaka Model

    • The workflow attempts to choose the appropriate files. Confirm these are the correct selections
    • The parameters have optimized default values and do not require modification for most experiments. Detailed descriptions can be found in the full manual

Input Read Collection
Select file collection for reads (FASTQ)

Reference Transcriptome
Select the reference transcriptome file (FASTA)

  1. Click Run Workflow to begin analysis

  2. Review output files

Called Variants
A report of all called variants from the analysis (VCF)

Consensus Sequence
A consensus sequence for each sample (FASTA)

QualiMap Report
An alignment quality report (HTML)

MultiQC Report
A compiled report of fastq, mapping, and variant QC statistics (HTML)

Please contact for any questions or assistance.