Parameterized syncmer schemes improve long-read mapping.

ABSTRACT:

Motivation

Sequencing long reads presents novel challenges to mapping. One such challenge is low sequence similarity between the reads and the reference, due to high sequencing error and mutation rates. This occurs, e.g., in a cancer tumor, or due to differences between strains of viruses or bacteria. A key idea in mapping algorithms is to sketch sequences with their minimizers. Recently, syncmers were introduced as an alternative sketching method that is more robust to mutations and sequencing errors.

Results

We introduce parameterized syncmer schemes (PSS), a generalization of syncmers, and provide a theoretical analysis for multi-parameter schemes. By combining PSS with downsampling or minimizers we can achieve any desired compression and window guarantee. We implemented

SUBMITTER: Dutta A 

PROVIDER: S-EPMC9645665 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature