Reads Binning Improves Alignment-Free Metagenome Comparison.

ABSTRACT: Comparing metagenomic samples is a critical step in understanding the relationships among microbial communities. Recently, next-generation sequencing (NGS) technologies have produced a massive amount of short reads data for microbial communities from different environments. The assembly of these short reads can, however, be time-consuming and challenging. In addition, alignment-based methods for metagenome comparison are limited by incomplete genome and/or pathway databases. In contrast, alignment-free methods for metagenome comparison do not depend on the completeness of genome or pathway databases. Still, the existing alignment-free methods, d2S and d2* , which model k-tuple patterns using only one Markov chain for each sample, neglect the heterogeneity within metagenomic data wherein po

SUBMITTER: Song K 

PROVIDER: S-EPMC6881972 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature