An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.

ABSTRACT: Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers

SUBMITTER: Deng X 

PROVIDER: S-EPMC4402509 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature