Capstone — Translational Genomics Project

Design, implement, and defend an end-to-end translational genomics project—data strategy, automated pipelines, analysis & interpretation, and submission-ready reporting.

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Session Index

Session 1 — Proposal & Data Strategy Session 2 — Pipeline Build & Automation Session 3 — Analysis, Viz & Validation Session 4 — Final Defense & Submission

Session 1

Fee: Rs 6300

Proposal & Data Strategy

Clinical question framing, outcomes, cohort design, consent & ethics

Theory

Data inventory, formats, metadata model, and governance plan

FAIR BioProject/BioSample ENA/GEO/SRA

Risk register, milestones, KPIs and acceptance criteria

RACI Issue Tracker Change Log

Session 2

Fee: Rs 8400

Pipeline Build & Automation

QC→align/assemble→call→annotate staged pipeline with configs

Snakemake/Nextflow Conda/Mamba Docker/Apptainer

Parameterization, profiles, CI/CD and run provenance capture

GitHub Actions MLflow/W&B checksum manifests

Dashboards and alerts for QC and runtime metrics

MultiQC Quarto JupyterLab

Session 3

Fee: Rs 11200

Analysis, Visualization & Validation

Differential expression/variant interpretation & pathway mapping

DESeq2/edgeR VEP/ANNOVAR GSEA/Reactome

Figures, tables and interactive notebooks for review

ggplot2/plotly Quarto JupyterLab

Validation checks, manual review & sign-off criteria

IGV QC gates Audit Trail

Session 4

Fee: Rs 14000

Final Defense & Submission

Oral defense with live demo and Q&A on design decisions

Theory + Practical

Export submission-ready bundle with provenance and metadata

RO-Crate/BagIt ENA/GEO/SRA PDF/CSV/TSV

Final report, checklist, and sign-off package

Quarto Zenodo DOI Change Log

Capstone — Translational Genomics Project | End-to-End Pipeline, Analysis & Submission Bundle

Build and defend an end-to-end translational genomics pipeline: ingest, QC, analysis, interpretation, and a submission-ready report bundle with full provenance.

Capstone — Translational Genomics Project