A randomized algorithm for aligning DNA sequences to reference genomes
Abstract
The alignment of reads generated by nextgeneration sequencers is an important problem in many biomedical applications. Although many methods have been proposed, we introduce a new randomized algorithm with the distinction of having high performance across a wide range of read lengths and base error rates. We utilize two FM indices to facilitate efficient bidirectional searching. Randomization allows us to estimate effectively key parameters, which ultimately account for the consistency in performance of the method. Our method by and large outperformed some of the recent and popular methods over a wide range of read lengths and base error rates. © 2013 IEEE.
Publication Title
2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013
Recommended Citation
Vo, N., Tran, Q., Niraula, N., & Phan, V. (2013). A randomized algorithm for aligning DNA sequences to reference genomes. 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013 https://doi.org/10.1109/ICCABS.2013.6629195
