Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.

ABSTRACT:

Background

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.

Results

We observe that the proportion of non-singletons k-mers decreases slowly with increasing k, and can be fitted by piecewise power-law functions with different exponents at different ranges of k. A slower decay at greater values for k indicates more limite

SUBMITTER: Li W 

PROVIDER: S-EPMC3927684 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature