q2-boots

q2-boots facilitates bootstrapped and rarefaction-based microbiome diversity analysis as a QIIME 2 plugin, enabling repeated resampling of feature tables and integration of computed diversity metrics into summary data artifacts compatible with downstream analytic tools.

Key Features:

• Core-metrics pipeline: The qiime boots core-metrics command resamples a feature table n times at a specified even sampling depth and computes alpha and beta diversity metrics on each resampled table.
• Multiple diversity metrics: The plugin supports thirty different alpha diversity metrics and twenty-two beta diversity metrics applied to bootstrapped or rarefied feature tables.
• Integrated output structure: Results are compiled into summary data artifacts identical in structure and type to single-table diversity analysis outputs, enabling seamless use of existing downstream analytic tools.
• Distance matrix integration: The plugin provides three options for integrating distance matrices computed on n resampled feature tables, addressing the structural complexity of pairwise distance averaging.
• Flexible command structure: Eight new actions are available through either a single QIIME 2 Pipeline command or more granular QIIME 2 Action commands.

Scientific Applications:

• Microbiome diversity analysis: q2-boots enables comprehensive assessment of alpha and beta diversity in microbiome datasets through bootstrapped and rarefaction-based resampling approaches.
• Robust diversity metric computation: The tool ensures all collected data is considered when computing microbiome diversity metrics by integrating results from multiple resampled tables.

Methodology:

Given a feature table, an even sampling depth, and the number of iterations to perform (n), the core-metrics command resamples the feature table n times and computes alpha and beta diversity metrics on each resampled table, with three alternative approaches for integrating the resulting distance matrices.