SeqEntropy: genome-wide assessment of repeats for short read sequencing.

ABSTRACT:

Background

Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free) reads at different lengths.

Methodology/principal findings

We define a metric H(k) to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k) to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k. In our experiments, we found that entropy loss correlates well with de-novo assembly coverage of a genome, and a score of ΔH(k)>1% indicates a sever

SUBMITTER: Chu HT 

PROVIDER: S-EPMC3609794 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature