Short-read DNA sequencing technologies have revolutionized bacterial genomics, but these technologies have limitations. It is easy to produce a high quality draft genome, but relatively costly and/or time consuming to complete a genome, so most bacterial genomes remain as drafts. Despite this, limitations of draft bacterial genomes for functional analysis have not been well assessed. To characterize the importance of missing and poor quality regions of draft genomes, analyses of COG categories and genes of medical importance were performed using analogous draft and complete genomes. A popular genomic island prediction tool, IslandViewer, was updated to allow draft genomes as input, and its ability to detect genomic islands in draft genomes was assessed. There are limitations to bacterial draft genome analysis, with respect to disproportionately missing certain types of genes. However, valuable information of medical interest, including virulence and antimicrobial resistance genes, can still be obtained from some draft genome datasets.
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Thesis advisor: Brinkman, Fiona
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