microclass

microclass classifies prokaryotic organisms from 16S rRNA gene sequences to provide taxonomic assignments for microbial community profiling.

Key Features:

• High-accuracy classifications: Implements advanced classification algorithms in C++ for efficient processing while providing access via an R interface.
• R package implementation: Provided as an R package exposing functions for classification and classifier training.
• Comprehensive training data set: Includes a ready-to-use function trained on an extensive, curated training data set to improve assignment accuracy.
• Customizable classifier training: Allows users to train classifiers using their own datasets.
• Uncertainty quantification: Quantifies uncertainties in taxonomic classifications to report confidence levels for assignments.
• Versatile input handling: Processes 16S rRNA gene sequences of varying lengths and qualities.

Scientific Applications:

• Microbial ecology: Provides taxonomic profiles to support studies of microbial diversity, community structure, and ecological functions.
• Environmental microbiology: Facilitates classification of 16S rRNA sequences from environmental samples with variable sequence quality and lengths.

Methodology:

Performs taxonomic classification using 16S rRNA gene sequence data, implements algorithms in C++ with an R interface, supplies a pre-trained classifier and supports user-trained classifiers, and quantifies classification uncertainty while handling sequences of varying lengths and qualities.