How genome complexity can explain the difficulty of aligning reads to genomes.

ABSTRACT:

Background

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship.

Results

We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently i

SUBMITTER: Phan V 

PROVIDER: S-EPMC4674900 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature