title: Get the most out of your metagenome: computational analysis of environmental sequence data.
abstract: New advances in sequencing technologies bring random shotgun sequencing of ecosystems within reach of smaller labs, but the complexity of metagenomics data can be overwhelming. Recently, many novel computational tools have been developed to unravel ecosystem properties starting from fragmented sequences. In addition, the so-called 'comparative metagenomics' approaches have allowed the discovery of specific genomic and community adaptations to environmental factors. However, many of the parameters extracted from these data to describe the environment at hand (e.g. genomic features, functional complement, phylogenetic composition) are interdependent and influenced by technical aspects of sample preparation and data treatment, leading to various pitfalls during analysis. To avoid this and complement existing initiatives in data standards, we propose a minimal standard for metagenomics data analysis ('MINIMESS') to be able to take full advantage of the power of comparative metagenomics in understanding microbial life on earth.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Konrad Ulrich
authors.initials: KU
authors.lastname: Foerstner
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000619:Aminohydrolases / Q000737:chemistry / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D019295:Computational Biology; D004783:Environmental Microbiology; D023281:Genomics / Q000379:methods* / Q000592:standards; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D000619:Aminohydrolases; C021867:nitrilase