{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/97641"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/97641","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"FPGA acceleration of short read alignment with high-level synthesis","abstract":"With the introduction of next-generation sequencing (NGS) technologies, DNA sequencing is becoming an increasingly widespread process. When performed on human patients, it can allow for the prediction and prevention of diseases. An essential part of this bioinformatics pipeline is short read alignment}, which refers to aligning short fragments of DNA to the large and expansive reference genome. This can be a very time-consuming process with much room for improvement. This thesis improves on Bowtie 2, an aligner that is already very popular and high-performing. 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