Using short k mers to quantify similarity between samples from targeted amplicon sequencing data

An amplicon panel and a whole species assignment method were developed to perform species assignment for the entire genus of Anopheles mosquitoes. k-mers can provide an objective way to compare highly diverged sequences, where multiple sequence alignment or alignment to a single reference genome tends to introduce bias towards better-represented clades in the panel and the reference species respectively. Moreover, k-mers provide a natural way to incorporate small indels in addition to SNPs, which considerably increases the power to distinguish between species when working with less than 10kb sequence.

To find out about how short k-mers can be used to quantify similarity between samples from targeted amplicon sequencing data, you can follow the step-by-step tutorial in our jupyter notebook.

👉 📖 You can read more about this method here.

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