The GenomeNext analysis pipeline can deliver accurate and reproducible genomic analysis results from FASTQ to VCF to annotation in under 2 hours for whole genomes, under 1 hour per exome, and 30 minutes per panel. The analysis pipeline follows best practices for both single sample and multisample variant discovery, and each step has been carefully designed to align raw sequence reads, refine alignment, clean up artifacts, and perform variant and genotype discovery with a high degree of confidence. The automated analysis platform features cost-effective solutions for clinical and research needs, regulatory compliance, secure storage, and collaboration for teams with unlimited user accounts.