Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction.

ABSTRACT:

Background

Enormous volumes of short read data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to the challenging problem of short read assembly. Thus alignment-free methods are needed for the comparison of NGS samples of short reads.

Results

Recently several k-mer based distance measures such as CVTree, d2(S), and co-phylog have been proposed or enhanced to address this problem. However, how to choose an optimal k value for those distance measures is not trivial since it may depend on different aspects of the sequence data. In this paper, we considered an alternative parameter-free approach: compression-based distance measure

SUBMITTER: Tran NH 

PROVIDER: S-EPMC4057587 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature