MetaSAMS—A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.

► MetaSAMS is a novel bioinformatics software platform for automated taxonomic and functional analysis of metagenome data. ► The system includes a pipeline consisting of three different classifiers that perform taxonomic profiling of metagenome sequences. ► In addition, MetaSAMS implements a functional pipeline based on contigs that automatically assigns functions to predicted coding sequences. ► MetaSAMS provides tools for statistical and comparative analyses based on taxonomic and functional annotations. ► It has been successfully applied for the analysis of a biogas-producing microbial community from a biogas-production plant.