The burgeoning frequency of genome sequencing in recent years is a testament to both the improvements in sequencing technologies and the utility of genomic analyses for biological discovery. The rapid proliferation in technological advancements and availability of complementary data types and techniques has obfuscated the optimal process of genome assembly and raised the barrier to entry to unprecedented levels. In this dissertation, we describe the genome assemblies performed for several marine teleosts and discuss the algorithms and applications required for genome assembly, including some of our specific contributions to the genome assembly and annotation space. In Chapter 1 and Chapter 2, we review the taxonomy, life history, and biogeography of the Roundjaw Bonefish (Albula glossodonta) and describe its genome assembly. The genome assemblies with some analyses are described for the Bluefin (Caranx melampygus) and Giant (Caranx ignobilis) Trevallies in Chapter 3 and Chapter 4, respectively. Chapter 5 and Chapter 6 define and assess algorithms for the annotation of simple sequence repeats in genomic sequences. Publicly available annotations of carbapenem-resistance plasmids were epidemiologically analyzed in Chapter 7. The resiliency of phylogenetic trees to the removal of taxa is explored with a new nodal stability metric and algorithm, TANOS, in Chapter 8. Finally, in Chapter 9, a review of and commentary on vertebrate genome assembly is presented with recommendations for new projects. The aim of this dissertation, and the final chapter in particular, is to explore genome assembly methods and reduce the barrier to entry for new entrants.