Abstract
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 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.
Code Availability AirLift source code and readme describing how to reproduce our results are available at https://github.com/CMU-SAFARI/AirLift.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
We have built a custom tool which is used by AirLift to improve the performance of our mechanism relative to existing works. We have further improved writing issues, and clarified sections that we received complaints about.