HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

ABSTRACT:

Motivation

Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial paradigm for this is to allow the value of k to vary; having a larger value of k where the graph is more complex and a smaller value of k where the graph would likely contain fewer spurious edges and vertices. One open problem that affects the practicality of this method is how to predict the value of k prior to building the de Bruijn graph. We show that optimal values of k can be predicted prior to assembly by using the information contained in a phylogenetically-close genome and therefore, help make the use of multiple values of k practical for gen

SUBMITTER: Shariat B 

PROVIDER: S-EPMC4304221 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature