Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

作者：Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis, loannis Iliopoulos · 发表于：Bioinformatics and Biology Insights · 年份：2015 · DOI：10.4137/bbi.s12462 · 被引用次数：422 · 研究领域：Microbial Community Ecology and Physiology、Genomics and Phylogenetic Studies、Gut microbiota and health

Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.