Metagenomics Study Design & Sample Prep — Hands-on

Design microbiome and metagenomics projects that give interpretable, publication grade results. This module walks through study design, sampling strategy, wet lab workflows, metadata capture and quality control so that downstream bioinformatics is robust and reproducible.

Metagenomics Study Design & Sample Prep

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Session Index

Session 1 — Microbiome & Metagenomics Study Design Session 2 — Sampling, DNA Extraction & Controls Session 3 — Library Prep, QC & Sequencing Strategy Session 4 — Mini Capstone: Study Charter & SOP Pack

Session 1

Fee: Rs 8800

Microbiome & Metagenomics Study Design

Framing microbiome and metagenomics questions

case control and cohort cross sectional and longitudinal clinical, environmental and industrial use cases

Experimental design and sources of bias

batch effects and run order confounding covariates technical and biological replicates

Choosing readout and platform

16S and ITS amplicon shotgun metagenomics long read ONT and PacBio extensions

Session 2

Fee: Rs 11800

Sampling, DNA Extraction & Controls

Sampling strategy and stabilisation

body site and matrix specific protocols cold chain and preservatives field and clinical collection kits

DNA extraction workflows and inhibitors

mechanical and chemical lysis host DNA depletion yield, purity and integrity checks

Contamination aware design and controls

blanks and negative controls mock communities and spike ins lab layout and clean room practices

Session 3

Fee: Rs 14800

Library Prep, QC & Sequencing Strategy

Amplicon and shotgun library preparation choices

primer schemes and variable regions fragmentation and insert size indexing and multiplexing plans

Library quality control and quantification

bioanalyzer and fragment analysis qPCR and fluorometric assays pooling and normalisation

Sequencing depth and run planning

read length and layout coverage and depth targets linking design to downstream analysis tools

Session 4

Fee: Rs 18800

Mini Capstone: Study Charter & SOP Pack

Drafting a contamination aware metagenomics study charter

theory plus guided practical

Checklists, SOP outlines and metadata templates

sample and field sheets laboratory workflow map sequencing request and run sheet

Deliverables: design document, sampling SOP and QC plan

PDF and editable templates spreadsheet or CSV planning sheets ready for downstream pipeline modules

PDF

Metagenomics Study Design & Sample Prep Training | Microbiome & Shotgun Project Planning

Metagenomics Study Design & Sample Prep — Hands-on