School of Bioinformatics · Microbial & evolutionary genomics
Microbiome & Metagenomics Analysis
Microbiome studies are common in medicine, agriculture and environmental science, and they come with statistical traps of their own. This course covers amplicon and shotgun workflows and the compositional statistics needed to analyse them.
Course overview
Microbiome & Metagenomics Analysis covers marker-gene (16S rRNA) and shotgun metagenomic studies: from demultiplexed reads to amplicon sequence variants, taxonomy, diversity, community comparisons and differential abundance.
Microbiome counts are compositional: an increase in one taxon lowers the measured share of all the others. The course teaches statistics that respect this, including centred log-ratio transforms and compositional differential-abundance methods, and the controls (blanks and mock communities) without which contamination can look like biology.
Learning outcomes
By the end of the course you will be able to:
- Process 16S data with QIIME 2 and DADA2
- Assign taxonomy and build phylogenies for diversity metrics
- Compute and compare alpha and beta diversity
- Test community differences with PERMANOVA and check its assumptions
- Run compositional differential-abundance analysis
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Bioinformatics Foundations
- Basic R
Best suited to
- Microbiology and environmental-science students
- Researchers running microbiome projects
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Amplicon versus shotgun
- Controls and contamination
- Sequencing depth
Topics
- QIIME 2 and DADA2
- ASVs versus OTUs
- Taxonomic classification
Topics
- Alpha diversity and rarefaction
- Bray–Curtis and UniFrac
- PCoA ordination
Topics
- PERMANOVA and its assumptions
- Compositional data and the CLR transform
- Differential-abundance methods
Topics
- Kraken2 and MetaPhlAn
- Functional profiling
- Assembly and binning overview
Topics
- Re-analysis
- Figures
- Reporting standards
Practical sessions and projects
Capstone project
Compare two microbial communities
Re-analyse a public 16S study and test whether the reported community differences hold up under compositional statistics.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Study design
Evaluate the controls, sequencing depth and metadata of three published microbiome studies.
- Amplicon processing
Denoise the QIIME 2 Moving Pictures data with DADA2 and assign taxonomy against SILVA.
- Diversity
Compute alpha diversity and rarefaction curves, then Bray–Curtis and UniFrac distances with PCoA ordination.
- Statistics
Test community differences with PERMANOVA, check dispersion, and run a compositional differential-abundance analysis.
- Shotgun metagenomics
Profile a shotgun sample with Kraken2 and MetaPhlAn and compare the two taxonomic profiles.
- Project: a published microbiome study
Re-analyse a published 16S study and test whether its reported community differences hold up.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Moving Pictures of the human microbiome: Amplicon processing and diversity analysis.QIIME 2 tutorial data (Caporaso et al. 2011)
- SILVA rRNA reference: Taxonomic classification.SILVA database
- Human Microbiome Project samples: Shotgun profiling exercises.HMP Data Portal
Core reading
- Bolyen E et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37:852–857.
- Callahan BJ et al. (2016). DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods 13:581–583.
- Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ (2017). Microbiome datasets are compositional: and this is not optional. Frontiers in Microbiology 8:2224.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Microbiome & Metagenomics Analysis, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Microbiome & Metagenomics Analysis
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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