Next generation sequencing reads comparison with an alignment-free distance.

ABSTRACT:

Background

Next Generation Sequencing (NGS) machines extract from a biological sample a large number of short DNA fragments (reads). These reads are then used for several applications, e.g., sequence reconstruction, DNA assembly, gene expression profiling, mutation analysis.

Methods

We propose a method to evaluate the similarity between reads. This method does not rely on the alignment of the reads and it is based on the distance between the frequencies of their substrings of fixed dimensions (k-mers). We compare this alignment-free distance with the similarity measures derived from two alignment methods: Needleman-Wunsch and Blast. The comparison is based on a simple assumption: the most correct distance is obtained by knowing in advance the reference sequence. Therefore, w

SUBMITTER: Weitschek E 

PROVIDER: S-EPMC4265526 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature