WAGS

WAGS processes short-read whole genome sequencing (WGS) data to perform variant discovery and annotation—identifying germline single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants (SVs)—across species provided an appropriate reference genome for veterinary and comparative genomics applications.

Key Features:

• Containerization: Containerized bioinformatics pipelines provide reproducible and portable computational environments for analysis.
• Comprehensive Variant Discovery: Identifies germline short variants (single nucleotide polymorphisms and insertions/deletions) and structural variants from short-read WGS data.
• Adaptability Across Species: Works with any species that has an appropriate reference genome for alignment and variant calling.
• Benchmarking and Best Practices: Incorporates methodologies adapted from the Genome Analysis Toolkit (GATK) and includes benchmarking data for preprocessing and joint genotyping.

Scientific Applications:

• Large-scale Variant Discovery: Enables discovery of germline variants from massively parallel short-read sequencing datasets at cohort scale.
• Veterinary and Comparative Genomics: Supports cross-species variant analysis and genetic studies within the veterinary community and comparative genomics research.
• Reproducible High-throughput Workflows: Facilitates reproducible processing and benchmarking of preprocessing and joint genotyping steps for high-throughput WGS projects.

Methodology:

Uses containerized bioinformatics pipelines with GATK-adapted methodologies and benchmarking data for preprocessing and joint genotyping to process short-read WGS and call germline SNPs, indels, and structural variants.