QIIME 2 plugin for calculating the Health Index from microbiome data. The plugin is based on the Gut Microbiome Health Index (GMHI) created by Gupta et al. 2020.
Taxonomic resolution for marker gene molecules can be improved by encompassing longer sequences. The Short MUlitple Reads Framework algorithm allows the scaffolding of multiple marker gene regions against a reference database; this plugin allows the constructionof a database, reconstruction, and extends the algorithm and introduces a way to generate a corresponding phylogenetic tree following reconstruction.
Data augmentation is a very useful and widely used method in data science. Especially, it can increase the sample size of the training set for machine learning models. Rarefy for Augment uses a simple rarefaction method to achieve data augmentation. The data augmentation should only be implemented on the training data set.
QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction. This simple "Average Rarefied Table" method has the potential to be an ideal alternative to the current one-shot rarefaction, as it can keep information and avoid variation of composition.