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Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Table 2

The number of 10-mers needed to hit all 30-long sequences in four genomes: Two bacterial genomes A. tropicalis, C. crescentus, the worm C. elegans and a mammal genome, H. sapiens.

The genome sizes are quoted after removing all Ns and ambiguous codes. We tested three algorithms: minimizers picking the lexicographically smallest 10-mer, minimizer picking the first in a random k-mer ordering, and selection using the set produced by DOCKS. In case of multiple DOCKS-selected 10-mers in the 30-long window, the lexicographically smallest was chosen. # mers is the number of distinct 10-mers selected, and avg. dist. is the average distance between two selected 10-mers.

Table 2

doi: https://doi.org/10.1371/journal.pcbi.1005777.t002