Nucleo Quality Control
  • 🌸Nucleo Quality Control
    • Workflow description
    • Requirements
    • Installation and Usage
    • Workflow inputs
      • Input for nucleo_qc.cwl
      • Input for nucleo_aggregate_visualize.cwl
    • Workflow outputs
    • ☀️Interpretation - MultiQC
      • Summary QC metrics
      • Coverage vs GC content
      • Capture Metrics
      • Insert Size
      • Target coverage distribution
      • Duplex Metrics
        • Duplex family sizes
        • Simplex family sizes
        • Duplex yield metrics
      • Mean Base Quality
      • Duplex Noise Metrics
      • Contamination
        • Hotspot in Normals
        • Major contamination
        • Minor contamination
        • Contributing sites
      • Fingerprinting
      • QC thresholds
  • 🇬🇷Interpretation - Athena Coverage report
    • Installation and running
    • Interpretation coverage report
      • Report details
      • Summary
      • Exons with <100% coverage at 500x
      • Per gene coverage summary
      • Per exon coverage
      • Coverage of Known Variants
      • Coverage per chromosome
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Nucleo Quality Control

Workflows that generates, aggregates, and visualizes quality control files for CMO-CH.

Introduction

This section aims to provide an introduction to the Nucleo Quality Control process along with installation and running instructions. The Nucleo QC process generated QC metrics for all type of BAM files generated by Nucleo, including collapsed, uncollapsed, duplex and simplex BAM files. The main outputs of the workflow are the MultiQC report and coverage report. Thorough intepretation of the output files can be found in this gitbook section.

Credits

  • CMO cfDNA Informatics Team

  • Clinical Bioinformatics

NextWorkflow description

Last updated 1 year ago

🌸
  • Introduction
  • Credits