National Workshop on Computational Metagenomics: Methods and Applications

National Workshop on Computational Metagenomics: Methods and Applications

Last date of Registration : 30th March, 2026

Mode of the Workshop : In – person

SKU: IIT Madras | Date : 7th - 9th April, 2026 Category:

Profile of the Instructors

Prof. Karthik Raman is a Professor in the Department of Data Science and AI at the Wadhwani School of Data Science & AI (WSAI), IIT Madras. His group develops scalable algorithmic and AI-driven frameworks for microbiome systems biology, in silico metabolic engineering, biological network design, and large-scale biological data analysis. Prof. Karthik also co-ordinates the Centre for Integrative Biology and Systems mEdicine (IBSE) and works closely with industry partners to apply data science and AI in pharma, healthcare, and life sciences. He teaches core undergraduate courses in programming, data structures, and algorithms, along with advanced courses in computational and systems biology, and has authored a textbook on Computational Systems Biology. 

Dr. Aarti Ravindran is a Postdoctoral researcher specialising in environmental microbiomes and systems biology. Holding an M.Sc. (Hons.) in Biological Sciences and an M.E. in Biotechnology from BITS Pilani, she earned her Ph.D. from Anna University, where she later served as Guest Faculty for two years. Her work at IIT focuses on metagenomic analyses across diverse ecosystems, including human gut, plant rhizosphere, marine, and built environments. She also works on constructing genome-scale metabolic models to evaluate microbial functional potential and community interactions.
Dr. Pratyay Sengupta is a Postdoctoral researcher in the Department of Data Science and AI at IIT Madras. He holds an M.S.–Ph.D. in Computational Biology from IIT Madras and a B.Tech in Biotechnology from the NIT Durgapur. He was a visiting scholar at the Biotechnology and Planetary Protection Group (BPPG), Jet Propulsion Laboratory, NASA. His research spans microbiome systems biology, microbial genomics, metagenomics, and taxonomy. He has described over 50 novel species and one novel genus. Pratyay develops data-driven methods to study microbial adaptation in extreme environments.

Session Details

Date of the Workshop : 7th - 9th April, 2026

Mode of the Workshop : In - person

Venue : NAC 2, IIT Madras

Timings (IST) : 09:00 am to 06:00 pm 

Schedule for the Workshop

Day Start Time Duration (min) End Time Event
1 Day 1: Apr 7th
Registration 9:00 60 10:00 Registration
Morning Session 1
 10:00 15 10:15 Opening Remarks: Welcome & Workshop Vision
10:15 45 11:00 Foundations of Metagenomics: Understanding the “what, why, and how” of metagenomics
Tea Break 11:00 15 11:15 Tea Break
Morning Session 2
 11:15 60 12:15 Introduction to 16S: Amplicon Theory & Discussion
Principles, experimental design, workflows, and common challenges
12:15 45 13:00 Installation & Getting Started
Command line interface (CLI) basics, Hands-on setup of tools and environments for amplicon analysis
Lunch Break 13:00 90 14:30 Lunch
Afternoon Session 1 14:30 90 16:00 Data in Action (Part I): Guided Hands-on Practicals
Working with real datasets and understanding core analysis steps, interpretation
Tea Break 16:00 15 16:15 Tea Break
Afternoon Session 2
 16:15 45 17:00 Data in Action (Part II): Workflow Completion
Guided analysis, troubleshooting,
Assignment
17:00 15 17:15 The Buffer Zone: Troubleshooting & Wrap-up
Additional support for participants and open queries
Evening Lecture 17:15 30 17:45 Beyond the Bench: Applications & Future Perspectives
Clinical, environmental, and industrial perspectives
2 Day 2: Apr 8th
Morning Session 1
 9:00 45 9:45 Introduction to shotgun sequencing: Long read sequencing, short read sequencing. Illumina, nanopore, oxford. - Advantages and disadvantages of all. What do we use and why?
9:45 75 11:00 Data quality checks and preprocessing:
Theory and installation of tools:
1. FASTQC
2. TRIMMOMATIC - Adaptor removal
3. KRAKEN2 - Taxonomic classification
4. BRACKEN
Tea Break 11:00 15 11:15 Tea Break
Morning Session 2 11:15 60 12:15 Continued:
5. CONTIG assembly
6. BINNING
7. Bin refinement
Lunch Break 12:15 90 13:45 Lunch
Afternoon Session 1
 13:45 45 14:15 Quality assement and Taxonomic classification:
1. CheckM
2. GTDBTk
14:15 45 15:00 Functional annotation
1. PROKKA
2. COGs
15:00 30 15:30 Assignment
Tea Break 15:30 15 15:45 Tea Break
Afternoon Session 2
 15:45 30 16:15 Buffer zone & Troubleshooting
16:15 30 16:45 Network analysis
Evening Lecture 16:45 30 17:15 ML in microbiome
3 Day 3: Apr 9th
Morning Session 1 9:00 60 10:00 Data pre-processing for statistical analysis
Tea Break 10:00 15 10:15 Tea Break
Morning Session 2 10:15 105 12 Diversity and differential abundance testing
Lunch Break 12:00 90 13:30 Lunch
Afternoon Session
 13:30 60 14:30 Hands-on analysis
Applying the statistical methods to demo data
14:30 30 15:00 Assignment
15:00 45 15:45 Guest lecture
High Tea 15:45 45 16:30 Tea Break
Evening Lecture 16:30 45 17:15 Guest lecture
Valedictory 17:15 15 17:30 Valedictory

Fees for the Workshop

Students and researchers from IIT Madras: Rs. 1180 (1000 + 18% GST)

Students and researchers from other colleges: Rs. 5900 (5000 + 18% GST)

Faculty: Rs. 8260 (7000 + 18% GST)

Intended Audience

Researchers / Faculty / UG students (3rd year and above) — with a background/interest in biology, and desirous of working with metagenomic data.

Certification Criteria

Compulsory attendance in all sessions and Completion of assignments given during the workshop.

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