Whole Genome Sequencing Analysis: Computational Pipelines and Workflows in Bioinformatics

Abstract

Whole genome sequencing (WGS) has revolutionized the biosciences and proven to be essential and invaluable to the identification of gene functions and their involvement in disease. The feasibility of WGS analysis is under the support of next generation sequencing (NGS) technologies, which require substantial computational and biomedical resources to acquire and analyze large and complex sequence data. Meanwhile, the rapid progress and innovation of NGS technology has successfully enabled the generation of large volumes of sequence data and reduced the expense for WGS. In this manuscript, we present an overview of computational pipelines and workflows for WGS analysis, illustrating the fundamental steps and methods of the workflow, including data preparation, alignment and assembly, variant calling, annotation, and analysis. Some commonly used tools and platforms are summarized for the implementation of genome sequencing. Next, we investigate the potential clinical applications of WGS for Mendelian diseases, complex diseases, and cancers in medical genetics. Finally, the current limitations and future development are discussed to provide guidance and direction for further exploration of WGS.