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Amplicon (16S/18S/ITS) Pipelines & Diversity Analysis Training | QIIME 2, DADA2, Taxonomy, Alpha/Beta Diversity

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Microbiome, Metagenomics & Environmental Bioinformatics >> Amplicon (16S/18S/ITS) Pipelines & Diversity Analysis Training | QIIME 2, DADA2, Taxonomy, Alpha/Beta Diversity

Amplicon (16S/18S/ITS) Pipelines & Diversity Analysis — Hands-on

Learn the end-to-end workflow for marker-gene sequencing (16S/18S/ITS) from raw reads to publication-ready figures. You'll denoise with DADA2/Deblur, assign taxonomy against SILVA/Greengenes2/UNITE, build trees, quantify alpha/beta diversity, and apply proper compositional statistics (ANCOM-BC, Songbird) for differential abundance. Includes a mini capstone on real datasets.

Amplicon (16S/18S/ITS) Pipelines & Diversity Analysis
Help Desk · WhatsApp
Session 1
Fee: Rs 8800
Experimental Setup, Primers & Data Intake
  • Marker choice & primer schemes
    • 16S V3–V4 / V4 18S / ITS1–ITS2 amplicon length & platforms
  • Data intake & QC setup
    • demultiplexing adapter/primer trimming FastQC / MultiQC
  • Project scaffolding
    • QIIME 2 artifacts metadata TSV (MIxS) reproducible folders
Session 2
Fee: Rs 11800
Denoising (DADA2/Deblur) , Chimera & ASVs
  • Read filtering & trimming strategy
    • quality profiles paired-end merging length thresholds
  • Denoising & chimera handling
    • DADA2 / Deblur consensus vs pooled uchime-vs / in-silico
  • ASV tables & prevalence filtering
    • feature tables contaminant detection (decontam) low-biomass care
Session 3
Fee: Rs 14800
Taxonomy, Phylogeny & Diversity
  • Taxonomic assignment & databases
    • SILVA / Greengenes2 UNITE (fungi) Naive Bayes / VSEARCH
  • Phylogeny & distance metrics
    • MAFFT / FastTree UniFrac (w/unweighted) Bray–Curtis / Jaccard
  • Alpha/Beta diversity & ordination
    • rarefaction & richness Shannon / Faith PD PCoA / NMDS / PERMANOVA
Session 4
Fee: Rs 18800
Compositional Stats, DA & Reporting
  • Normalization & transformations
    • CLR / rCLR / rarefy?
  • Differential abundance (compositional)
    • ANCOM-BC / ALDEx2 DESeq2 (caveats) Songbird / Qurro
  • Reporting & reproducibility
    • QIIME 2 visualizations Quarto / R Markdown model cards & data dictionary


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