ArticleBioinformatics (Oxford, England)2023
Effects of spaced k-mers on alignment-free genotyping.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- ProGenFixer: An Ultrafast and Accurate Tool for Correcting Prokaryotic Genome Sequences Using a Mapping-Free Algorithm.Computational and structural biotechnology journal · 2026Article
- Article
- Comparative analysis of RAD-seq methods for SNP discovery and genetic diversity assessment in oil seed crop safflower.Scientific reports · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Article
- A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review.Frontiers in microbiology · 2024Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAlignment-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.
resultsWe 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 low coverage data. If applications implement effective algorithms for hashing of spaced k-mers, spaced k-mers have the potential to become an useful technique in k-mer based genotyping. AVAILABILITY AND IMPLEMENTATION: The source code of our proposed tool MaskedPanGenie is openly available on https://github.com/hhaentze/MaskedPangenie.
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