VAMPS

VAMPS visualizes and analyzes microbial population structures from marker-gene next-generation DNA sequencing data to support taxonomic assignments, taxonomy-independent clustering, and community diversity analyses.

Key Features:

• Data upload and quality filtering: Accepts marker gene sequences and associated metadata and performs quality filtering of reads.
• Taxonomic and clustering assignments: Assigns reads to taxonomic classifications and to taxonomy-independent sequence clusters.
• Filtering and dataset selection: Supports selection and filtering of datasets by taxonomy and abundance and the use of private, collaborative, or public project data.
• Analytic methods and visualizations: Produces a range of analytic outputs and visualizations for exploring microbial diversity and community relationships.
• Data sharing and metadata exchange: Enables sharing of sequence data and metadata among researchers to facilitate comparative analyses across biomes.
• Scalability: Handles large next-generation sequencing datasets on the order of 10^5–10^8 reads.

Scientific Applications:

• Molecular microbial ecology: Characterize microbial community dynamics across time and space in ecological studies.
• Comparative biome analyses: Compare microbial assemblages across biomes and support collaborative hypothesis generation and testing.
• Diversity and community structure investigation: Analyze community composition, taxonomic structure, and sequence-similarity–based cluster patterns.

Methodology:

Computational steps explicitly include quality filtering of reads, taxonomic assignment, taxonomy-independent clustering of sequences, filtering by taxonomy and abundance, and generation of analytic visualizations.