Evaluation of viral genome assembly and diversity estimation in deep metagenomes.

ABSTRACT:

Background

Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.

Results

We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA , which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an import

SUBMITTER: Aguirre de Carcer D 

PROVIDER: S-EPMC4247695 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature