Amplicon (16S/ITS/18S) Analysis & Compositional Data Principles — Hands-on

Learn how to take raw 16S/ITS/18S reads through quality control, denoising, feature table construction, taxonomy and phylogeny, while respecting the compositional nature of microbiome data. This module focuses on practical amplicon workflows with QIIME 2 and related tools, plus the statistical mindset needed for downstream analyses.

Amplicon (16S/ITS/18S) Analysis & Compositional Data Principles

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Session Index

Session 1 — From Raw Reads to Quality Filtered Data Session 2 — Denoising, Features & Taxonomy Session 3 — Compositional Data & Normalization Session 4 — Mini Capstone: End-to-End Amplicon Workflow

Session 1

Fee: Rs 8800

From Raw Reads to Quality Filtered Data

Understanding amplicon read structure and metadata linkage

barcodes and primers paired end overlap sample and run metadata

Quality profiles and trimming strategies

Phred quality curves adapter and primer removal cutadapt and other tools

Demultiplexing and initial quality control in QIIME 2

import and manifest files per sample sequence counts QC summaries and reports

Session 2

Fee: Rs 11800

Denoising, Feature Tables & Taxonomy

Denoising with DADA2 or Deblur

ASVs versus OTUs error models chimera handling

Feature table construction and filtering

samples versus features matrix prevalence and abundance filters rare features and noise

Taxonomic assignment and phylogeny building

reference databases (SILVA, Greengenes, UNITE) naive Bayes classifiers phylogenetic trees for diversity metrics

Session 3

Fee: Rs 14800

Compositional Data & Normalization Strategies

Why microbiome data are compositional

library size and relative scale closure and spurious correlations Aitchison geometry intuition

Normalization and transformation options

rarefaction and its limits relative abundance CLR, ALR and ILR transforms

Preparing feature tables for downstream diversity and differential analyses

filtering low depth samples handling zeros exporting to R and Python

Session 4

Fee: Rs 18800

Mini Capstone: End-to-End Amplicon Workflow

Designing and running a small 16S workflow

guided theory plus practical

Quality reports, feature tables and taxonomy summaries

QIIME 2 visualizations exported tables basic diversity preview

Compositional checklist and documentation for next modules

pipeline and parameter log data export and backup FAIR and reproducibility notes

PDF

Amplicon (16S/ITS/18S) Analysis & Compositional Data Principles Training | QIIME 2, Denoising & Compositional Stats

Amplicon (16S/ITS/18S) Analysis & Compositional Data Principles — Hands-on