Next-generation sequencing (NGS) is a robust high-throughput method which can expedites the sequencing of the base pairs in DNA or RNA samples rapidly and efficiently. As the cost of NGS has declined, whole-genome sequencing (WGS) has become continuously appealing due to a large amount of genetic information it reveals. The emergence of WGS using NGS technology is a revolutionary advancement in almost all areas of life sciences, ranging from health and medical to agricultural and forestry applications. NGS-based WGS technology has been implemented for several years in Indonesia, especially in the genomics study of infectious disease-related microbes. Yet, it continues to thrive and extensively be used in the recent emergence and widespread transmission of SARS-CoV-2. This present brief review will discuss WGS platforms and their applications that have been documented in Indonesia in recent times. Moreover, the challenges and future prospects of research and development of WGS in Indonesia will also be highlighted herein. [ABSTRACT FROM AUTHOR]