Authors: Faria Mahmud, Khaled Noor, Sabrina Yasmin, Tanmoy Hossain
Abstract: The unprecedented growth of genomic data driven by next-generation sequencing technologies has imposed complex computational demands on bioinformatics infrastructure. UNIX-based systems comprising Solaris, AIX, and Linux form the backbone of genomic data processing environments due to their reliability, performance, and rich toolchain support. However, their default configurations are seldom tuned for the high-throughput, memory-intensive, and I/O-sensitive nature of genomic workloads. This review explores the critical need for infrastructure-level optimization in UNIX environments to support workflows such as sequence alignment, variant calling, and RNA-Seq analysis. It presents a detailed examination of system-level strategies including NUMA-aware CPU allocation, memory page tuning, ZFS and GPFS storage optimization, network throughput enhancement, and scheduler configuration using SLURM and PBS. Case studies from academic and clinical domains highlight the real-world impact of these optimizations on pipeline performance and resource efficiency. The article also addresses compliance considerations under HIPAA and GDPR, demonstrating how audit controls and data encryption can be embedded into UNIX configurations. Looking forward, the review outlines emerging trends such as AI-assisted infrastructure tuning, containerization of genomic workflows, and the integration of persistent memory and cloud bursting strategies. Collectively, this review provides system administrators, bioinformatics engineers, and IT architects with a comprehensive blueprint for transforming UNIX platforms into high-performance, secure, and scalable environments tailored for genomics.
DOI: https://doi.org/10.5281/zenodo.15846976
