title: Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.
abstract: 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.
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Anastasis
authors.initials: A
authors.lastname: Oulas
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece. ; Department of Biology, University of Ghent, Ghent, Belgium. ; Department of Microbial Ecophysiology, University of Bremen, Bremen, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Pavloudi
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Paraskevi
authors.initials: P
authors.lastname: Polymenakou
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece.
authors.forename: Georgios A
authors.initials: GA
authors.lastname: Pavlopoulos
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece.
authors.forename: Nikolas
authors.initials: N
authors.lastname: Papanikolaou
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Kotoulas
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
authors.forename: Christos
authors.initials: C
authors.lastname: Arvanitidis
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Iliopoulos
keywords: computational tools; data analysis; metagenomics; next-generation sequencing