AirLift: a fast and comprehensive technique for remapping alignments between reference genomes

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buir.contributor.authorAlkan, Can
buir.contributor.orcidAlkan, Can|0000-0002-5443-0706
dc.citation.epage9
dc.citation.spage1
dc.contributor.authorKim, Jeremie S.
dc.contributor.authorFirtina, Can
dc.contributor.authorCavlak, Meryem Banu
dc.contributor.authorÇalı, Damla Şenol
dc.contributor.authorHajinazar, Nastaran
dc.contributor.authorAlser, Mohammed
dc.contributor.authorAlkan, Can
dc.contributor.authorMutlu, Onur
dc.date.accessioned2025-02-18T13:56:07Z
dc.date.available2025-02-18T13:56:07Z
dc.date.issued2024-08-19
dc.departmentDepartment of Computer Engineering
dc.description.abstractAirLift 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
dc.identifier.doi10.1109/TCBB.2024.3433378
dc.identifier.eissn1557-9964
dc.identifier.issn1545-5963
dc.identifier.urihttps://hdl.handle.net/11693/116390
dc.language.isoEnglish
dc.publisherIEEE
dc.relation.isversionofhttps://www.doi.org/10.1109/TCBB.2024.3433378
dc.rightsCC BY 4.0 (Attribution 4.0 International Deed)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.source.titleIEEE/ACM Transactions on Computational Biology and Bioinformatics
dc.subjectBioinformatics
dc.subjectRemapping
dc.subjectRead mapping
dc.subjectLiftover
dc.titleAirLift: a fast and comprehensive technique for remapping alignments between reference genomes
dc.typeArticle

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