Salvatore Alaimo, University of Catania, Catania, Italy

Techniques and Algorithms for Microbiome analysis through Next-Generation Sequencing
In recent years, the development of next-generation sequencing (NGS) techniques have given rise to a considerable simplification of the analysis of genomes and transcriptomes yielding also the ability to evaluate bacterial and viral genomes present in a host with a single analysis. This allowed wider studies, which take into account the full genetic content of a sample, including what comes from microbial communities (meta-genomics). Such techniques are therefore offering major unexpected opportunities. In this tutorial we will start by describing some standard techniques to pre-process NGS sequencing data. We will, then, illustrate some pipelines which manipulate such data in order to extract information about microbiome composition together with viral integration sites in host genome. We will finally describe some methods to infer differentially abundant characteristics among metagenomes and their functional information. All this will be enriched, where possible, with examples demonstrating their usefulness in a clinical context.

Bibliography

Accurate genome relative abundance estimation based on shotgun metagenomic reads. Plos One, 2011

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome medicine, 2015

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies. Bioinformatics and biology insights, 2015