Limitations of Genomic Analysis on Novel Species
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2021
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Haverford College. Department of Computer Science
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Thesis
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eng
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Open Access
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Abstract
For widely studied species such as humans, fruit flies, and mice, there are many sequenced genomes, but for novel species, only afew or a singular processed genome is available. Being able to study novel species is important to understand their environmental impact, in the case of invasive species, or their genetic relation to other species but they pose the greatest difficulty to study. Genetic sequences are created using assemblers and assembling the genome for a diploid species is a computationally complex task which is why diploid assemblers create a phased collapsed genome that contains similar genetic information. Applications of Pairwise Sequential Markovian Coalescent (PSMC) modeling for population size inference and Phylogenetic tree generation for building a species family tree become more difficult with novel species and it is not clear how to proceed. Other tools exist, such as Read Mapping and NCBI's Blast, that provide the initial steps to the first two tools mentioned but are not well integrated with them. As a proof of concept, we applied Read Mapping with PSMC analysis and Blast with Phylogenetic tree construction on the novel species, the Spotted Lanternfly, to investigate the feasibility of these tools on a phased genome. At least for this genome, our analysis shows there to be significant limitations due to computational run time and with the processed output of our pipeline. More work is needed to better integrate various tools to analyze novel species.