Estimation of viral richness from shotgun metagenomes using a frequency count approach.

ABSTRACT:

Background

Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA gene with which to estimate richness, and so contig spectra are employed to measure the number of virus taxa in a given community. A contig spectrum is generated from a viral shotgun metagenome by assembling the random sequence reads into groups of sequences that overlap (contigs) and counting the number of sequences that group within each contig. Current tools available to ana

SUBMITTER: Allen HK 

PROVIDER: S-EPMC3869190 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature