METAREP

METAREP uses Solr/Lucene to provide queryable analysis and comparative visualization of annotated metagenomic datasets for taxonomic and functional profiling.

Key Features:

• Solr/Lucene-based indexed search: Enables rapid querying across large annotated metagenomic collections using an SQL-like query syntax.
• Graphical summaries: Generates visual summaries highlighting top taxonomic and functional classifications.
• Integrative ontology and taxonomy browsing: Provides browsing and linkage through Gene Ontology (GO), NCBI Taxonomy, and KEGG Pathway Browser.
• Comparative analysis: Compares multiple datasets at various functional and taxonomic levels and reports absolute and relative counts.
• Statistical and multivariate analyses: Performs statistical tests and multidimensional scaling for comparative studies.
• Clustering and heatmaps: Produces heatmap and hierarchical clustering plots to identify patterns across datasets.
• Export formats: Exports summaries as tab-delimited files and plots in PDF format.
• Collaborative data management: Supports shared analysis and result dissemination among research teams.

Scientific Applications:

• Comparative metagenomic analysis: Compare annotated metagenomic datasets to detect taxonomic and functional differences between samples.
• Taxonomic profiling: Profile microbial community composition using NCBI Taxonomy classifications.
• Functional profiling and pathway analysis: Annotate and explore gene functions and pathways via Gene Ontology and KEGG Pathway Browser.
• Multivariate and clustering analyses: Identify sample grouping and patterns using statistical tests, multidimensional scaling, heatmaps, and hierarchical clustering.
• Multi-investigator data sharing: Facilitate shared analyses and dissemination of results within collaborative projects.

Methodology:

Indexed search using Solr/Lucene with an SQL-like query syntax; integration and browsing via Gene Ontology (GO), NCBI Taxonomy, and KEGG Pathway Browser; application of statistical tests and multidimensional scaling; generation of heatmaps and hierarchical clustering; export to tab-delimited files and PDF.