Work

PLA-index: A k-mer Index Exploiting Rank Curve Linearity

Year: 2024

Type: conference-paper

Abstract: -mer in the suffix array of the human genome to within 255 positions. Furthermore, we demonstrate the potential of our approach to impact a variety of downstream applications. First, the PLA-index halves the time of binary search on the suffix array of the human genome. Second, the PLA-index reduces the space of a direct-access lookup table by 76 percent, without increasing the run time. Third, we plug the PLA-index into a state-of-the-art read aligner Strobealign and replace a 2 GiB component with a PLA-index of size 1.5 MiB, without significantly effecting runtime. The software and reproducibility information is freely available at https://github.com/medvedevgroup/pla-index.

Source: PubMed

DOI: 10.4230/lipics.wabi.2024.13

Authors: Abrar, Md. Hasin, Medvedev, Paul

Institution: Pennsylvania State University

Language: English

Topic: Algorithms and Data Compression

Subfield: Artificial Intelligence

Field: Computer Science

Domain: Physical Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences

Awards: Frameworks: Re-Engineering Galaxy for Performance, Scalability and Energy Efficiency, A k-mer-based search engine for sequencing databases, Leveraging k-mer sketching statistics to enhance metagenomic methods and alignment algorithms