Re-purposing software for functional characterization of the microbiome

摘要: BACKGROUND Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows software. For analysis the microbiome, typically begin with taxonomic classification microorganisms that are present in given environment. Additional investigation is then required to uncover functionality microbial community, order characterize its currently or potentially active biological processes. Such functional metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we directly compare reads functionally annotated database. However, since frequently match multiple sequences equally well, analyses benefit from hierarchical annotation tree, e.g. where assigned lowest unit. RESULTS To facilitate microbiome analysis, re-purpose well-known tools allow us perform direct read added hierarchy. enable this, develop tree-shaped hierarchy representing molecular function subset Gene Ontology structure. We use this replace standard phylogenetic taxonomy used by assign query accurately possible tree. demonstrate simulated experimental datasets, reveal new insights. CONCLUSIONS improved re-purposing range already well-established, conjunction either protein nucleotide reference databases. leverage advances speed, accuracy efficiency have been made translate these benefits rapid microbiomes. While focus on specific set commonly methods, approach has broad applicability across other sequence tools. hope becomes routine consideration during development. Video abstract.