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- All Subjects: Bioinformatics
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
Description
Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled into chromosomes using the 2014 Callithrix jacchus genome as a reference. Then, using that same genome as a reference, 13 of the chromosomes were reverse complimented to be continuous with the 2014 Callithrix jacchus genome. The N50 statistics of the assembly were calculated and found to be 124 Mb. Quality scores were run for the final genome using referee and visualized with a bar plot, with 99% of sites scoring above 0. Heterozygosity was also calculated and found to be 0.3%. Finally, the final version of the genome was visually compared to the 2017 Callithrix jacchus genome and the GRCh38 human genome. This genome was submitted to the NCBIs database to await further approval.
ContributorsJohnson, Joelle Genevieve (Author) / Cartwright, Reed (Thesis director) / Stone, Anne (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Analyzing human DNA sequence data allows researchers to identify variants associated with disease, reconstruct the demographic histories of human populations, and further understand the structure and function of the genome. Identifying variants in whole genome sequences is a crucial bioinformatics step in sequence data processing and can be performed using multiple approaches. To investigate the consistency between different bioinformatics methods, we compared the accuracy and sensitivity of two genotyping strategies, joint variant calling and single-sample variant calling. Autosomal and sex chromosome variant call sets were produced by joint and single-sample calling variants for 10 female individuals. The accuracy of variant calls was assessed using SNP array genotype data collected from each individual. To compare the ability of joint and single-sample calling to capture low-frequency variants, folded site frequency spectra were constructed from variant call sets. To investigate the potential for these different variant calling methods to impact downstream analyses, we estimated nucleotide diversity for call sets produced using each approach. We found that while both methods were equally accurate when validated by SNP array sites, single-sample calling identified a greater number of singletons. However, estimates of nucleotide diversity were robust to these differences in the site frequency spectrum between call sets. Our results suggest that despite single-sample calling’s greater sensitivity for low-frequency variants, the differences between approaches have a minimal effect on downstream analyses. While joint calling may be a more efficient approach for genotyping many samples, in situations that preclude large sample sizes, our study suggests that single-sample calling is a suitable alternative.
ContributorsHowell, Emma (Co-author) / Wilson, Melissa (Thesis director) / Stone, Anne (Committee member) / Phung, Tanya (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05