A simple refined DNA minimizer operator enables 2-fold faster computation.

ABSTRACT:

Motivation

The minimizer concept is a data structure for sequence sketching. The standard canonical minimizer selects a subset of k-mers from the given DNA sequence by comparing the forward and reverse k-mers in a window simultaneously according to a predefined selection scheme. It is widely employed by sequence analysis such as read mapping and assembly. k-mer density, k-mer repetitiveness (e.g. k-mer bias), and computational efficiency are three critical measurements for minimizer selection schemes. However, there exist trade-offs between kinds of minimizer variants. Generic, effective, and efficient are always the requirements for high-performance minimizer algorithms.

Results

We propose a simple minimizer operator as a refinement of the standard canonical minimizer. It t

SUBMITTER: Pan C 

PROVIDER: S-EPMC10868324 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature