AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
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.
Authors
- Nastaran Hajinazar (ORCID: https://orcid.org/0000-0003-2817-0223)
- Damla Senol Cali (ORCID: https://orcid.org/0000-0002-3665-6285)
- Jeremie S. Kim (ORCID: https://orcid.org/0000-0001-6153-9008)
- Onur Mutlu (ORCID: https://orcid.org/0000-0002-0075-2312)
- Meryem Banu Cavlak (ORCID: https://orcid.org/0000-0003-4475-6945)
- Can Fırtına (ORCID: https://orcid.org/0000-0002-6548-7863)
- Can Alkan (ORCID: https://orcid.org/0000-0002-5443-0706)
- Mohammed Alser (ORCID: https://orcid.org/0000-0002-6117-3701)
Institutions
- Bilkent University (TR)
- ETH Zurich (CH)
- Carnegie Mellon University Australia (AU)
Publication Details
- Journal
- IEEE Transactions on Computational Biology and Bioinformatics
- Published
- 2024-08-19
- DOI
- https://doi.org/10.1109/tcbb.2024.3433378
- Citations
- 4
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.23