SARS-CoV-2, the pathogen responsible for the ongoing Coronavirus Disease 2019 pandemic is a novel human-infecting strain of Betacoronavirus. The outbreak that initially emerged in Wuhan, China, rapidly spread to several countries at an alarming rate leading to severe global socio-economic disruption and thus overloading the healthcare systems. Owing to the high rate of infection of the virus, as well as the absence of vaccines or antivirals, there is a lack of robust mechanisms to control the outbreak and contain its transmission. Rapid advancement and plummeting costs of high throughput sequencing technologies has enabled sequencing of the virus in several affected individuals globally. Deciphering the viral genome has the potential to help understand the epidemiology of the disease as well as aid in the development of robust diagnostics, novel treatments and prevention strategies. Towards this effort, we have compiled a comprehensive protocol for analysis and interpretation of the sequencing data of SARS-CoV-2 using easy-to-use open source utilities. In this protocol, we have incorporated strategies to assemble the genome of SARS-CoV-2 using two approaches: reference-guided and de novo. Strategies to understand the diversity of the local strain as compared to other global strains have also been described in this protocol.