Wastewater samples are challenging substrates for nucleic acid extraction, and choice of extraction method will determine the success of downstream analysis. Extraction methods must be able to address high levels of inhibitory substances and achieve extraordinary sensitivity to provide the best possible detection of SARS-CoV-2. Even with ideal extraction, SARS-CoV-2 RNA from wastewater often remains highly fragmented and is often at a low copy number. However, with optimized sequencing techniques, it is still possible to produce high quality SARS-CoV-2 libraries from wastewater. This talk will discuss how to optimize sample extraction and NGS workflows for SARS-CoV-2 wastewater analysis.