Browsing by Author "Kim, Jeremie S."

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    AirLift: a fast and comprehensive technique for remapping alignments between reference genomes
    (IEEE, 2024-08-19) Kim, Jeremie S.; Firtina, Can; Cavlak, Meryem Banu; Çalı, Damla Şenol; Hajinazar, Nastaran; Alser, Mohammed; Alkan, Can; Mutlu, Onur
    AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4×. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants