Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.

ABSTRACT:

Background

With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a reference genome alignment-based methods are not applicable. However it is still possible to study the evolutionary relationship of unassembled genomes based on NGS data.

Results

We present a parameter-free alignment-free method, called Under2, based on variable-length patterns, for the direct comparison of sets of NGS reads. We define a similarity measure using variable-length patterns, as well as reverses and reverse-complements, along with their statistical a

SUBMITTER: Comin M 

PROVIDER: S-EPMC4168702 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature