Hongyi Xin1, Sunny Nahar1, Richard Zhu1, John Emmons2, Gennady Pekhimenko1, Carl Kingsford3, Can Alkan4, Onur Mutlu5. 1. Computer Science Department. 2. Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA. 3. Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA. 4. Department of Computer Engineering, Bilkent University, Bilkent, Ankara 06800, Turkey and. 5. Computer Science Department, Department of Electrical and Computer Engineering.
Abstract
MOTIVATION: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the ability of the mapper in selecting less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds. RESULTS: We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently-occurring set of x seeds in an L-base-pair read in [Formula: see text] operations on average and in [Formula: see text] operations in the worst case, while generating a maximum of [Formula: see text] seed frequency database lookups. We compare OSS against four state-of-the-art seed selection schemes and observe that OSS provides a 3-fold reduction in average seed frequency over the best previous seed selection optimizations. AVAILABILITY AND IMPLEMENTATION: We provide an implementation of the Optimal Seed Solver in C++ at: https://github.com/CMU-SAFARI/Optimal-Seed-Solver CONTACT: hxin@cmu.edu, calkan@cs.bilkent.edu.tr or onur@cmu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the ability of the mapper in selecting less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds. RESULTS: We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently-occurring set of x seeds in an L-base-pair read in [Formula: see text] operations on average and in [Formula: see text] operations in the worst case, while generating a maximum of [Formula: see text] seed frequency database lookups. We compare OSS against four state-of-the-art seed selection schemes and observe that OSS provides a 3-fold reduction in average seed frequency over the best previous seed selection optimizations. AVAILABILITY AND IMPLEMENTATION: We provide an implementation of the Optimal Seed Solver in C++ at: https://github.com/CMU-SAFARI/Optimal-Seed-Solver CONTACT: hxin@cmu.edu, calkan@cs.bilkent.edu.tr or onur@cmu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Mohammed Alser; Jeremy Rotman; Onur Mutlu; Serghei Mangul; Dhrithi Deshpande; Kodi Taraszka; Huwenbo Shi; Pelin Icer Baykal; Harry Taegyun Yang; Victor Xue; Sergey Knyazev; Benjamin D Singer; Brunilda Balliu; David Koslicki; Pavel Skums; Alex Zelikovsky; Can Alkan Journal: Genome Biol Date: 2021-08-26 Impact factor: 13.583