Capstone: End-to-End Microbiome Project — Hands-on

Bring together everything you learned across microbiome, metagenomics and AMR analytics in one end to end capstone. You will scope a realistic project, design the analysis, implement pipelines for amplicon or shotgun data, apply statistics and machine learning where appropriate, and prepare publication and FAIR ready outputs and documentation.

Capstone: End-to-End Microbiome Project

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Session Index

Session 1 — Project Scoping & Study Design Session 2 — Pipeline Implementation & QC Session 3 — Ecological, Functional & ML Insights Session 4 — Final Deliverables & Presentation

Session 1

Fee: Rs 8800

Project Scoping & Study Design

Selecting a capstone use case and framing questions

clinical, environmental or industrial scenarios primary and secondary analysis questions hypotheses, endpoints and constraints

Study design, metadata model and data audit

group structure, replication and covariates MIxS aligned metadata checklist data quality scan and gap identification

Analysis plan and workflow sketch for the project

amplicon or shotgun pipeline choices diversity, differential and network analyses timeline, checkpoints and risk management

Session 2

Fee: Rs 11800

Pipeline Implementation & QC

Raw read processing and quality control for the project

trimming, filtering and contaminant checks negative and positive control evaluation run level QC plots and decisions

Taxonomic and functional profiling or MAG pipeline

feature tables, taxonomy and pathway tables resistome or virome layers if relevant pipeline logging and parameter capture

Normalisation, filtering and data readiness for modeling

compositional aware transforms and offsets prevalence and sparsity decisions project data objects ready for analysis scripts

Session 3

Fee: Rs 14800

Ecological, Functional & ML Insights

Diversity, ordination and differential abundance views

alpha and beta diversity panels PERMANOVA, constrained ordination and drivers feature level contrasts and effect sizes

Functional, resistome or network style summaries

pathway, module or AMR profile plots simple co occurrence or correlation networks linking signals back to project questions

Optional ML or predictive modeling for the project

train test splits and cross validation simple classifiers or regressors where relevant feature importance and interpretation caveats

Session 4

Fee: Rs 18800

Final Deliverables & Presentation

Project report and slide deck structure

background, methods, results and interpretation

Reproducible artefacts and FAIR ready packaging

notebooks or scripts with environment files data dictionaries and codebooks submission checklist for archives or journals

Deliverables: report, slides and project bundle

PDF or HTML project report presentation slides or poster outline data plus code bundle for future reuse

PDF

Capstone End-to-End Microbiome Project Training | From Study Design to FAIR Outputs

Capstone: End-to-End Microbiome Project — Hands-on