Amphibian extinctions and extirpations are caused by a variety of factors, including the Chytridiomycosis panzootic and its causative agents: the batrachochytrids Batrachochytrium salamandrivorans (Bsal) and Batrachochytrium dendrobatidis (Bd). Until recently, the genomic basis for the batrachochytrids’ evolution and their virulence was largely unknown. To investigate their virulence and evolution, a high-quality genome assembly was needed. Prior to 2022, only a highly fragmented short-read assembly of Bsal’s genome assembly had been generated and made available, largely owing to its repeat-richness. In 2022, a new assembly based on deep nanopore long-read sequencing provided a much-needed improvement in both contiguity and completeness. Achieving this improvement relied not only on the choice of assembler and polishing-strategy, but also on extensive quality control and preprocessing of the reads. Here, we discuss the initial stages of genome assembly, focusing specifically on preassembly and quality control considerations and protocols using both long and short reads are described, detailing the methodology and underlying rationale for each step.