GreedyMini: generating low-density DNA minimizers.

ABSTRACT:

Motivation

Minimizers are the most popular k-mer selection scheme in algorithms and data structures analyzing high-throughput sequencing (HTS) data. In a minimizer scheme, the smallest k-mer by some predefined order is selected as the representative of a sequence window containing w consecutive k-mers, which results in overlapping windows often selecting the same k-mer. Minimizers that achieve the lowest frequency of selected k-mers over a random DNA sequence, termed the expected density, are desired for improved performance of HTS analyses. Yet, no method to date exists to generate minimizers that achieve minimum expected density. Moreover, for k and w values used by common HTS algorithms and data structures, there is a gap between densities achieved by existing selection schemes

SUBMITTER: Golan S 

PROVIDER: S-EPMC12261476 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature