Effects of spaced k-mers on alignment-free genotyping.

ABSTRACT:

Motivation

Alignment-free, k-mer based genotyping methods are a fast alternative to alignment-based methods and are particularly well suited for genotyping larger cohorts. The sensitivity of algorithms, that work with k-mers, can be increased by using spaced seeds, however, the application of spaced seeds in k-mer based genotyping methods has not been researched yet.

Results

We add a spaced seeds functionality to the genotyping software PanGenie and use it to calculate genotypes. This significantly improves sensitivity and F-score when genotyping SNPs, indels, and structural variants on reads with low (5×) and high (30×) coverage. Improvements are greater than what could be achieved by just increasing the length of contiguous k-mers. Effect sizes are particularly large for l

SUBMITTER: Hantze H 

PROVIDER: S-EPMC10311327 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature