Metagenomics - a guide from sampling to data analysis

A bioinformatician's guide to metagenomics.

As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by...

Analysis of metagenomics data

Improved sampling of diverse environments and advances in the development and application of next-generation sequencing technologies is accelerating the rate at which new metagenomes are produced. Over the past few years, the major challenge associated with metagenomics has shifted from generating to analyzing sequences. Metagenomic analysis includes the identification, and functional and evolu...

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes

BACKGROUND Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contam...

A Concise Guide to Compositional Data Analysis

Imaging as a guide to tissue sampling

When assessing a patient with lung cancer, it is important to stage the tumor in order to determine prognosis and direct appropriate therapy. Although imaging findings, particularly with CT and PET, can suggest the correct tumor stage, imaging is imperfect in this regard; enlarged and/or hypermetabolic lymph nodes may require sampling for confirmation of presumed tumor stage. A major role for i...