16S 18S ITS Amplicon Sequencing Analysis — Hands-on

Learn how to process 16S, 18S and ITS amplicon sequencing data from raw FASTQ files to publication ready figures. This module covers denoising, chimera handling, feature table generation, taxonomy assignment, diversity analysis and basic differential abundance for microbiome studies.

16S 18S ITS Amplicon Sequencing Analysis

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Session Index

Session 1 — Amplicon Concepts & Experimental Design Session 2 — Denoising, ASVs and Taxonomy Session 3 — Diversity, Ordination & Differential Abundance Session 4 — Mini Capstone: End to End Amplicon Workflow

Session 1

Fee: Rs 8800

Amplicon Concepts & Experimental Design

Marker gene choices and primer schemes

16S V3 V4 and V4 V5 regions 18S and ITS for fungi eukaryotes primer bias and coverage

Amplicon specific study design considerations

replication and blocking index hopping and cross talk read depth and sample size

FASTQ structure and initial QC thinking

paired end vs single end quality score profiles adapter and primer removal strategy

Session 2

Fee: Rs 11800

Denoising, ASVs and Taxonomy

Denoising pipelines and chimera handling

DADA2 workflow Deblur overview chimera removal strategies

ASVs vs OTUs and feature tables

clustering thresholds sparse count matrices filtering and prevalence rules

Taxonomy assignment and reference databases

SILVA and Greengenes UNITE for ITS naive Bayes and alignment based classifiers

Session 3

Fee: Rs 14800

Diversity, Ordination & Differential Abundance

Alpha and beta diversity workflows

Shannon and Faith PD UniFrac and Bray Curtis rarefaction and normalization options

Ordination and community patterns

PCA and PCoA NMDS and clustering PERMANOVA and dispersion tests

Differential abundance and compositional methods

ANCOM and ALDEx2 DESeq2 style models log ratio transforms CLR and ILR

Session 4

Fee: Rs 18800

Mini Capstone: End to End Amplicon Workflow

From raw FASTQ to feature table and taxonomy

theory plus guided practical

Core diversity plots and summary figures

QIIME2 and R based visualisation taxonomy barplots ordination scatter plots

Deliverables: workflow notes, parameter log and report

QIIME2 artifacts and R scripts HTML or PDF report ready to plug into downstream modules

PDF

16S 18S ITS Amplicon Sequencing Analysis Training | Denoising, Taxonomy & Diversity

16S 18S ITS Amplicon Sequencing Analysis — Hands-on