Metabarcoding & Species Richness Estimation — Hands-on

Build rigorous metabarcoding workflows from primer design to biodiversity estimation. You will learn marker/primer trade-offs, QC & denoising to ASVs, robust taxonomic assignment, and statistically sound diversity/richness estimation (alpha/beta, rarefaction/extrapolation, Chao/ACE/breakaway) . Emphasis on controls, bias correction, and MIxS-compliant, reproducible reporting for ecological and biomonitoring studies.

Metabarcoding & Species Richness Estimation

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Session Index

Session 1 — Study Design, Markers & Controls Session 2 — QC, Denoising & Taxonomy (ASVs) Session 3 — Diversity, Rarefaction & Richness Session 4 — Bias Correction, Standards & Reporting

Session 1

Fee: Rs 8800

Study Design, Markers & Controls

Marker/primer selection & amplicon strategy

16S/18S/ITS/COI trade-offs amplicon length & resolution in silico primer checks

Sampling design & replication

spatial/temporal replicates power & coverage goals blocking/stratification

Controls & contamination safeguards

field/kit blanks, negatives mock communities/spike-ins tag-jump mitigation

Session 2

Fee: Rs 11800

QC, Denoising & Taxonomy (ASVs)

Read processing & ASV/OTU inference

cutadapt/fastp, merging DADA2/UNOISE/VSEARCH chimera removal & LULU curation

Taxonomic assignment & references

SILVA/PR2/UNITE/BOLD/MIDORI naive Bayes / IDTAXA / BLAST LCA confidence & curation

Decontamination & thresholds

decontam prevalence/frequency min depth/read filters replicate concordance

Session 3

Fee: Rs 14800

Diversity, Rarefaction & Richness Estimation

Alpha/beta diversity & ordinations

Hill numbers/Q profiles Aitchison/UniFrac choices PERMANOVA caveats

Rarefaction & extrapolation

coverage-based rarefaction iNEXT/vegan toolchains curves & stopping rules

Richness estimators & uncertainty

Chao1/ACE/breakaway Good–Turing & unseen species CIs, bootstrap & bias checks

Session 4

Fee: Rs 18800

Bias Correction, Standards & Reproducible Reporting

Biases & mitigation

primer/amplification bias copy number corrections contamination diagnostics

Standards, metadata & submissions

MIxS/ENVO fields ENA/SRA & checklisting audit trails & SOPs

Reporting & deliverables

Quarto/knitr notebooks tables/figures + env files stakeholder-ready summaries

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Metabarcoding & Species Richness Estimation Training | ASVs, iNEXT, Chao/ACE/Breakaway & Bias-Aware Reporting

Metabarcoding & Species Richness Estimation — Hands-on