YACHT

YACHT performs a statistical test for detecting microbial presence or absence in metagenomic samples based on ANI (Average Nucleotide Identity).

Key Features:

• ANI-based divergence modeling: Accounts for sequence divergence between reference and sample genomes in terms of ANI.
• Incomplete sequencing depth correction: Adjusts for incomplete sequencing depth when determining genome presence.
• Hypothesis testing framework: Provides a statistical hypothesis test with associated confidence for determining presence or absence of a reference genome in a sample.
• Statistical power quantification: Quantifies statistical power and its variation with changing parameters.

Scientific Applications:

• Metagenomic community profiling: Determines which genomes from a reference database are present or absent in a given sample metagenome.
• Low-abundance organism detection: Addresses interpretation difficulties for low-abundance organisms in the noisy tail of incorrect predictions.
• Reference database gap handling: Accounts for incomplete reference databases that rarely contain exact replicas of environmentally derived metagenome genomes.

Methodology:

YACHT uses a statistical framework that accounts for sequence divergence between reference and sample genomes in terms of ANI as well as incomplete sequencing depth to provide a hypothesis test for genome presence. The approach was validated using simulated and real data experiments.