Capstone — Applied Microbiome Project — Hands-on

Apply everything learned across microbiome and metagenomics modules in a guided capstone. You will scope a realistic question, design or refine an analysis plan, run contamination aware and compositional workflows, and deliver a concise, reproducible report and slide deck suitable for collaborators, hiring managers or academic supervisors.

Capstone — Applied Microbiome Project

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Session Index

Session 1 — Project Scoping & Dataset Audit Session 2 — Workflow Design, QC & Preprocessing Session 3 — Core Analysis, Figures & Interpretation Session 4 — Final Report, Slides & Reproducible Package

Session 1

Fee: Rs 8800

Project Scoping & Dataset Audit

Selecting a project and framing the question

choice of gut, environmental or clinical theme biological, clinical or One Health motivation clear primary and secondary endpoints

Dataset, metadata and readiness audit

what is already available vs to be collected sample numbers, groups and time points missingness, batch and obvious caveats

Ethics, consent and data sharing boundaries (concept level)

clinical vs public environmental datasets de identification and safe reporting repository and collaboration constraints

Session 2

Fee: Rs 11800

Workflow Design, QC & Preprocessing

Choosing and sketching the pipeline

amplicon vs shotgun vs MAG centric path tools already used in earlier modules simple diagrams of steps and inputs

Quality control and contamination checks

read level QC and trimming choices negative controls and potential contaminants basic run and batch diagnostics

Preprocessing into analysis ready tables

feature tables, taxonomic and pathway profiles normalisation and transformations for compositional data clean, linked sample and metadata sheets

Session 3

Fee: Rs 14800

Core Analysis, Figures & Interpretation

Exploratory and ecological summaries

alpha and beta diversity panels ordination plots coloured by key covariates basic time course or gradient views if relevant

Differentials, networks or multi omics (as suited to project)

differential abundance or composition aware methods simple co occurrence or association views optional metabolome or host covariate overlays

Interpreting patterns without over claiming

effect sizes, uncertainty and limitations biological and applied meaning of key results clear next steps and follow up experiments

Session 4

Fee: Rs 18800

Final Report, Slides & Reproducible Package

Structuring a short report or manuscript style summary

introduction, methods, results and discussion skeleton

Building a slide deck for non specialist stakeholders

story arc and key messages figure selection and simplification next steps and decision support framing

Deliverables: notebook, report, slides and project bundle

analysis notebook with comments PDF or HTML report plus slide deck organised folder with data, metadata and readme

PDF

Capstone — Applied Microbiome Project Training | End-to-End Microbiome Analysis & Reporting

Capstone — Applied Microbiome Project — Hands-on