nf-core-sarek

nf-core-sarek performs end-to-end detection and annotation of germline and somatic variants from whole-genome (WGS), whole-exome (WES) and targeted gene panel sequencing to support genomic analyses including tumor/normal and relapse sample studies.

Key Features:

• Supported data types and samples: Processes WGS, WES and targeted gene panels and supports tumor/normal pairs and relapse samples across genomes with an available reference (including human and mouse).
• GATK best-practices: Adheres to GATK best-practice recommendations for read alignment and pre-processing.
• Variant detection spectrum: Identifies and annotates germline and somatic single-nucleotide variants (SNVs), insertions and deletions (indels), and structural variants.
• Copy-number, ploidy and purity analyses: Includes analyses for tumor sample purity, ploidy estimation and copy-number variation.
• Quality metrics reporting: Produces extensive quality metrics to support validation and reproducibility of variant calls.
• Containerized reproducibility and environments: Supports Docker and Singularity containers and Conda environments for deployment and reproducible execution.
• Workflow implementation: Implemented in Nextflow as a modular workflow integrating multiple variant-calling and annotation tools.

Scientific Applications:

• Cancer genomics: Detection of somatic mutations, structural variants and copy-number changes and assessment of tumor purity and ploidy in tumor/normal and relapse samples.
• Hereditary disease and germline variant discovery: Identification and annotation of germline SNVs and indels from WES, WGS and targeted panels.
• Model organism and comparative genomics: Application to human, mouse or any species with an available reference genome for comparative or model organism studies.
• Precision medicine research: Supporting discovery of clinically relevant variants for translational and precision-medicine investigations.

Methodology:

Implemented in Nextflow; leverages Docker, Singularity and Conda environments; follows GATK best-practice read alignment and pre-processing recommendations and integrates multiple variant-calling and annotation tools in a modular workflow.