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Abstract
Sarcocystis neurona is an obligate intracellular parasite and the main agent behind equine protozoan myeloencephalitis a disease of critical importance to the equine industry. To facilitate the S. neurona genome project this study developed a bioinformatics framework that included assembly of the apicoplast genome, assembly and testing multiple transcriptome assembly algorithms and evaluating each to identify the superior assembly. Also, a pipeline for annotation of the nuclear genome was developed and its effectiveness was demonstrated via annotation of the S. neurona apicoplast genome. Finally, in order to facilitate study of and access to, the S. neurona genome, a database, SarcoDB, was created. It is intended that the results of this study will greatly aid in our understanding of the parasite, Sarcocystis neurona.