DCS Tools: A high-performance, resource-efficient and scalable computing suite for population-scale genomic analysis and data compression

Abstract

The advent of population-scale genomics has created significant bottlenecks in computational infrastructure and storage. Traditional BWA-GATK Best Practices require massive resources, while most existing acceleration solutions depend on specialized hardware like GPUs or FPGAs, increasing costs and limiting deployment. To address this, we developed DCS Tools, a high-performance suite optimized for standard CPU architectures. DCS Tools processes a 30X WGS sample from raw FASTQ to variant calls in just 1.79 hours on a 32-thread instance--a 16-fold speedup over traditional pipelines without additional hardware. The suite integrates DPGT for million-scale joint calling and introduces SeqArc and VarArc, which reduce storage footprints by up to 80% (FASTQ) and 66% (VCF) compared to GZIP. DCS Tools offers a cost-effective, hardware-agnostic solution for petabyte-scale genomic analysis.