Related Experiment Video
Updated: May 25, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances
Eduardo Charvel1, Isaac Thomas2, Homère J Alves Monteiro3
1Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, USA.
None:
Understanding ecological change requires robust, inexpensive methods for monitoring populations. One approach is using low-coverage genome sequencing (genome skimming) to compute genetic diversity via assembly-free, alignment-free, k-mer-based methods to compute genomic distances from shotgun sequences using the intersection of k-mer sets. Skmer extended this approach to genome skims by modeling coverage and error. However, these methods ignore genome repetitiveness, hampering population genetic distance calculation. Here, we mathematically derive the expected intersection size between k-mers sampled from two repetitive genomes, accounting for repeats, coverage, and errors, leading to the method ReSkmer. Our experiments show highly accurate distances despite sampling highly repetitive genomes.
Related Concept Videos
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Gene Conversion
Crossing Over
Evolutionary Relationships through Genome Comparisons
Homologous Recombination
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

