Fig. 1

Overview of Taxonomer architecture and user interface. a Taxonomer’s architecture. Raw FASTA, FASTQ, or SRA files (with or without gzip compression) are the input for Taxonomer. For paired-end data, mate pairs are analyzed jointly. Taxonomer consists of four main modules. The “Binner” module categorizes (“bins”) reads into broad taxonomic groups (host and microbial) followed by comprehensive microbial and host gene expression profiling at the nucleotide (“Classifier” module) or amino acid-level (“Protonomer” and “Afterburner” modules). Normalized host gene expression (gene-level read counts) and microbial profiles can be downloaded. Read subsets can be downloaded for custom downstream analyses (b) Taxonomer web-service. To further remove barriers for academic and clinical adoption of metagenomics, we developed a web interface for Taxonomer that allows users to stream sequencing read files (stored locally or http accessible) to the analysis server and interactively visualize results in real time. Main features are described in grey boxes. Taxonomic classification of bacteria, fungi, and viruses is visualized as a sunburst graph (center), in which the size of a given slice represents the relative abundance at the read level. Taxonomic ranks are shown hierarchically with the highest rank in the center of the graph. Sequences that cannot be classified to the species level, either because they are shared between taxa or represent novel microorganisms, are collapsed to the lowest common ancestor and shown as part of slices that terminate at higher taxonomic ranks (e.g. genus, family)