Workflows - Viral Diversity
Phages, the viruses that infect bacteria, are the most abundant biological entities in the biosphere, with an estimated 1031 particles on the planet. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. The metagenomic approach allows the study of viral communities without cultivation and estimating their diversity. The alpha diversity workflow assesses the biodiversity of a single viral community (termed α- diversity) while Gamma diversity predicts the total biodiversity over two or more viral communities (termed γ-diversity). The alpha diversity and gamma diversity tools in CAMERA predict viral diversities using six rank-abundance distributions (broken stick, exponential, logarithmic, lognormal, niche pre-emption, and power law) from metagenomic sequences.
Alpha Diversity:
Estimates a viral community structure and diversity based on contig spectrum calculated from metagenomic information obtained from one viral community.
Gamma Diversity:
Estimates overall viral community structure and diversity in combined viral communities based on contig spectrum calculated from metagenomic sequences obtained from multiple viral communities.
Workflow Components:
The Alpha and Gamma Diversity workflows are composed of several components, including:
- Circonspect: Produces contig spectra, useful for the estimating viral diversity in metagenomes. It uses an external assembly program and a bootstrap technique to automate the generation of contig spectra and cross-contig spectra.
- GASS (Genome relative Abundance and Average Size): Calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.
- PHACCS (PHAge Communities from Contig Spectrum): Models the structure and estimates the diversity of uncultured viral communities, based on the contig spectrum.
Notes:
- The current reference library utilized by the Apha and Gamma Diversity workflows is a custom phage database built and maintained by the Rohwer Lab at San Diego State University.
- To adjust default parameters, click on the “Advanced Parameters” tab on the workflow submission form.