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. 2024 Dec 26;41(1):btae743.
doi: 10.1093/bioinformatics/btae743.

The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation

Haozhe Neil Duan  1 , Gavin Hearne  1 , Robi Polikar  2 , Gail L Rosen  1
Affiliations

The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation

Haozhe Neil Duan et al. Bioinformatics. .

Abstract

Motivation: This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

Results: NBC++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

Availability and implementation: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.

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Figures

Figure 1.
Figure 1.
The Phylum and Order (over 2% relative abundance) composition of the human sample is shown. Standard and Extended databases have more concordance than Basic and Standard databases.
See this image and copyright information in PMC

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