Alignment-Free Genome and Metagenome Comparison Based on NGS Reads

Abstract

Next generation sequencing (NGS) technologies have generated enormous amount of shotgun read data and assembly of the reads can be challenging, especially for organisms without template sequences. We develop novel alignment-free and assemble-free statistics for genome and metagenome comparison and study their limit behaviors. The statistics were used to study the evolutionary relationships among 13 tree species whose templates sequences are not known. They were also used to classify metagenomes and metatranscriptomes. In all applications, our novel statistics yield clustering that is consistent with biological knowledge. Thus, our statistics provide a powerful alternative approach for genome and metagenome comparison based on NGS short reads.