myPhyloDB

myPhyloDB stores, processes, and analyzes 16S metagenomics and microbial community data for comparative microbial ecology studies.

Key Features:

• Data Storage and Management: Archives raw sequencing files and organizes projects and samples for downstream analysis.
• Data Processing Capabilities: Accepts uploaded pre-processed data and includes an integrated Mothur pipeline for automated processing of raw sequencing data.
• Analytical Tools: Provides statistical and multivariate analyses including analysis of covariance (ANCOVA), t-tests, linear regression, differential abundance testing using DESeq2, and principal coordinates analysis (PCoA).
• Normalization Techniques: Implements normalization methods including rarefaction, DESeq2-based normalization, and proportion-based normalization.
• Comparative Analysis Features: Enables comparative analyses of taxonomic abundance, species richness, and diversity at user-selected taxonomic levels across projects and sample types such as human-associated microbiomes, gut microbiome studies, air, soil, and water samples.

Scientific Applications:

• Human-associated microbiome analysis: Analyzes taxonomic abundance, richness, and diversity in human-associated microbiome datasets.
• Gut microbiome studies: Performs differential abundance and diversity comparisons in gut microbiome studies using DESeq2 and multiple normalization strategies.
• Environmental microbiome analysis: Characterizes and compares microbial community composition and diversity in air, soil, and water samples.

Methodology:

Processing of raw sequencing data via an integrated Mothur pipeline; support for uploaded pre-processed data; normalization by rarefaction, DESeq2, or proportion-based methods; statistical analyses including ANCOVA, t-tests, linear regression, differential abundance testing with DESeq2, and ordination by PCoA.