######################################################################## Downstream Analysis ######################################################################## Basic plots --------------------------------- zAMP provides basic plots to help researchers quickly assess and interpret their sequence processing results using pipeline. The pipeline automatically generates various visualizations and summary outputs, including: 1. Quality Control (QC) Metrics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - **Reads Filtering Summary**: A bar plot showing the number of processed and retained reads per sample, enabling users to assess data quality across samples. 2. Taxonomic Overview ~~~~~~~~~~~~~~~~~~~~~ - **Krona Plots**: Interactive, hierarchical visualizations of taxa detected in the samples, allowing users to explore taxonomic compositions interactively. 3. Diversity Analysis ~~~~~~~~~~~~~~~~~~~~~ - **Rarefaction curve**: Metrics such as Observed, Shannon, Simpson, and Chao1 indices, plotted across sequencing depths to evaluate within-sample diversity. Advanced Downstream Analysis with zAMPExplorer ---------------------------------------------- While zAMP provides foundational analyses, its companion tool, `zAMPExplorer `_, offers a more interactive and detailed exploration of the data. The tool uses the Phyloseq object (output from zAMP), allowing users to: 1. Enhanced Quality Check ~~~~~~~~~~~~~~~~~~~~~ - Review sequencing depth and filter samples with low read counts. - Inspect detailed read statistics and filtering results. 2. Taxonomic Exploration ~~~~~~~~~~~~~~~~~~~~~ - Dive into the taxa composition of individual samples or groups. - Create compositional barplots and abundance heatmaps to visualize relative abundances. 3. Diversity Analysis ~~~~~~~~~~~~~~~~~~~~~ - Perform advanced alpha and beta diversity analyses with group-wise comparisons. - User can perform statistical comparisons of alpha diversity using the Wilcoxon rank-sum test, and beta diversity using methods such as PERMANOVA (Permutational Multivariate Analysis of Variance) and betadisper (analysis of multivariate homogeneity of group dispersions) to assess the significance of observed differences between sample groups. 4. Advanced Statistical Features ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - **Differential Abundance Testing**: Identify taxa that are differentially abundant across experimental conditions. - **Community Typing**: Conduct Dirichlet multinomial Mixtures (DMM) modeling to determine the optimal number of microbial community types. - **Multivariate Analysis**: Perform constrained ordination technique (CAP). 5. User-Friendly Visualization ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Interactive plots and user-driven filtering options make it easier to tailor analyses to specific research questions. The streamlined workflow between zAMP and zAMPExplorer ensures that users can transition seamlessly from initial data processing to more detailed statistical analyses. The Phyloseq object generated by zAMP serves as the input for zAMPExplorer, maintaining data consistency and reproducibility throughout the pipeline. zAMPExplorer Usage ~~~~~~~~~~~~~~~~~~ After running zAMP, simply load the resulting Phyloseq object into zAMPExplorer. By combining zAMP's reproducible pipeline with zAMPExplorer's advanced interactivity, user can perform comprehensive microbiota profiling with minimal setup. zAMPExplorer instructions are available here: `https://github.com/metagenlab/zAMPExplorer `_.