Low-cost short-read genome assembly allows diverse downstream genetic analyses on non-model fishes

Many genetic analyses require or are improved by utilizing a reference genome for the focal organism. However, given that producing the long-read data that is traditionally used in the assembling process remains expensive, we still lack genomic information for the great majority of non-model species. Here, we test the performance of four commonly used tools (ABySS, HipMer, SOAPdenovo, and SPAdes) in generating short-read de novo assemblies from eight marine fish species. We demonstrate that assemblies with high values for N50 and BUSCO Complete and Single Copy are possible using only short-read data. Overall, successful genome assembly from short reads allows for a large suite of downstream genetic analyses and represents an affordable avenue for studying non-model organisms, especially for large-scale projects, programs monitoring genetic diversity, or studies with limiting resources.