Sarek

Sarek performs end-to-end variant calling, annotation, and quality reporting for whole-genome, whole-exome, and targeted sequencing to support germline and somatic (tumor/normal) analyses including SNVs, indels, structural variants, tumor heterogeneity assessment, and karyotyping.

Key Features:

• Modular Design: A configurable, modular workflow structure that enables selection and combination of analysis modules for specific research needs.
• Comprehensive Variant Analysis: Identification and annotation of single-nucleotide variants (SNVs), insertion/deletion variants (indels), and structural variants, including support for tumor heterogeneity and karyotyping from paired tumor/normal samples.
• Robust Portability: Implemented in Nextflow with compatibility for Docker, Singularity, and Conda execution environments to enable reproducible execution across compute platforms.
• Reproducibility and Best Practices: Read alignment and pre-processing follow Genome Analysis Toolkit (GATK) best-practice recommendations and the workflow produces extensive quality metrics reporting.
• Support for Multiple Sequencing Data Types: Supports whole-genome sequencing (WGS), whole-exome sequencing (WES), and gene panel data.

Scientific Applications:

• Precision Medicine: Enables variant discovery and annotation required for genomic analyses that inform clinical and research decisions in precision medicine.
• Cancer Genomics: Facilitates somatic mutation profiling, assessment of tumor heterogeneity, and karyotyping from paired tumor/normal samples for cancer research.
• Germline and Population Studies: Supports germline variant detection across WGS, WES, and panel datasets for genetic and population-scale studies.

Methodology:

Implemented in Nextflow; performs read alignment and pre-processing according to GATK best-practice recommendations, followed by variant calling (SNVs, indels, structural variants), annotation and extensive quality metrics reporting, and supports execution via Docker, Singularity and Conda.