Kuura

Kuura automates the analysis of whole exome and whole genome sequencing data through a multi-stage workflow that generates high-confidence variant calls via consensus from multiple variant callers.

Key Features:

• Multi-caller variant consensus: Integrates GATK HaplotypeCaller, DeepVariant, VarScan2, FreeBayes, and Strelka2 to produce a consensus call file of high-confidence variants.
• Containerized deployment: Uses Nextflow and Docker for workflow management and deployment.
• Single parameters file: Centralizes configuration to enhance reproducibility of results.
• Modular extensibility: Allows addition or updating of tools and amendment of parameters.

Scientific Applications:

• WES and WGS variant calling: Optimized for both whole exome and whole genome sequencing data analysis.
• Standardized variant detection: Provides a reproducible, standardized approach for variant calling across different research projects.

Methodology:

The workflow consists of four analysis stages: quality control; mapping to reference genome and quality score recalibration; variant calling and variant recalibration; and variant consensus and annotation.