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Welcome to YACHT!

The README documentation contains instructions about installation, downloading pre-built databases, making your own databases, and running the tool. This wiki gives a higher-level description of the YACHT approach and also provides some use-cases demonstrating its utility.

YACHT: a brief description

YACHT stands for Yes/No Answers to Community membership via Hypothesis Testing. It is a mathematically rigorous hypothesis test that determines the presence or absence of each genome from a reference database in a given metagenomic sample under user-defined threshold values. Specifically, the user is required to provide the following values in addition to a reference database and an unprocessed metagenomic sequencing sample: 1. a false negative rate $a$ which controls the sensitivity of the method. 2. A value $A$ that indicates the threshold of Average Nucleotide Identity (ANI) above which two organisms will be considered biologically identical. 3. the coverage $c$ needed for a given microbe's genome to be considered present in the sample. YACHT then outputs the a file indicating the presence and absence of each of the organisms among those in the reference database in the sample. For more detailed explanation of the method, refer to the associated preprint.

YACHT workflow

Use case examples

To showcase the use of YACHT, we provide three examples of application for taxonomic identificatin for metagenomic studies here.

In particular, we highlight three scenarios: Low Abundance Samples , metagenome-assembled genome (MAG) fishing, and Synthetic Metagenomes. Through these examples, we illustrate how YACHT’s flexible parameters—such as k-size, ANI, and minimum coverage—can be adjusted to influence results and provide deeper insight into the taxonomic composition of these samples.