Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a longer read is more likely to be uniquely mapped to the reference genome, a quantitative analysis of the influence of read lengths on mappability has been lacking. To address this question, we evaluate the k-mer distribution of the human reference genome. The k-mer frequency is determined for k ranging from 20 bp to 1000 bp.
k-mers read alignment next-generation sequencing repeat sequences genome redundancy long-tail distribution