🖥️ HPC Resource Cockpit > Workshop Participants: Click here to log in to your pre-configured HPC server environments for the hands-on sessions.
📅 Official Workshop Portal > Check here for the live schedule, announcements, and full event details.
Welcome to the official repository for the Five-day Hands-on Workshop Program on Bioinformatics for One Health and Pathogen-Specific Research.
This repository contains all the computational notebooks, scripts, and datasets required for the hands-on sessions.
Organised by: CSIR-Institute of Genomics and Integrative Biology, New Delhi Funded by: Indian Council of Medical Research (ICMR)
The curriculum is divided into daily folders. Each folder contains the Jupyter/Colab Notebooks (.ipynb) and a data/ subdirectory for that day's specific exercises.
DAY_1/- Linux Basics & Environment SetupDAY_2/- Genome Assembly Workflow & Quality AssessmentDAY_3/- Comparative Genomics, Variant Calling, & Functional EnrichmentDAY_4/- Antimicrobial Resistance (AMR) & Microbiome AnalysisDAY_5/- Isoform Analysis & Graph-Augmented AI/ML
All hands-on sessions will utilize preconfigured HPC/Cloud-based platforms for reproducibility. However, participants are expected to bring their own laptops for the practical training sessions.
System Requirements:
- A modern web browser (Chrome/Firefox/Safari) for accessing Google Colab.
- A stable internet connection.
- Note for macOS users: Your MacBook's native Terminal runs Zsh by default; we will be utilizing standard Bash environments in our Colab/HPC instances, so keep standard Linux syntax in mind!
Workshop materials and sample datasets will be provided within each daily folder.
Navigating One Health Bioinformatics
- Morning: Inauguration, Talk on Harnessing Genomic Technologies.
- Hands-on 1A & 1B: Linux Basics for Bioinformatics, Command-line navigation, core Unix utilities, BASH scripting, and Conda package management.
- Evening: CSIR-IGIB Bio-bank & HPC Facility visit.
From Raw Data to Complete Genomes
- Morning: Talks on Pathogenomics, AI-enabled insights, and Principles of genome assembly.
- Hands-on 2A: Quality assessment and visualization (FastQC, Fastp, MultiQC).
- Hands-on 2B: Viral Genome Assembly (Setu pipeline, Spades) and Completeness Check (QUAST/BUSCO).
Deciphering Genetic Relationships
- Morning: Understanding Pathogen Diversity.
- Hands-on 3A: SNP & Variant Calling, Mapping Sequencing Reads.
- Hands-on 3B: Sequence Alignment, Phylogenetic tree Construction.
- Spotlight Tools: Pathway enrichment analysis with getEnrich and Chromosomal rearrangement with Chitra.
- Hands-on 3C: croSSRoad pipeline for SSR-Driven Comparative Genomics.
Genomic Approaches for Antimicrobial Resistance
- Morning: ARKbase: Antimicrobial Resistance Knowledgebase 1.0
- Hands-on 4A & 4B: Exploring AMR databases, genome-based resistance tools, and analytical workflows.
- Hands-on 4C: Microbiome Analysis and Marker Feature Identification using MarkerML.
From Genomes to Public Health [cite: 212]
- Morning: Talks on Alternate Transcript Isoforms and Graph-Augmented AI/ML for AMR.
- Afternoon: Valedictory & Certificate Distribution, followed by Delhi Darshan.
Thanks goes to these wonderful people (emoji key):
This project follows the all-contributors specification. Contributions of any kind welcome!
"Alone we can do so little; together we can do so much." — Helen Keller
A special thank you to all the unnamed volunteers, administrative staff, and supporting members behind the scenes. This 5-day intensive workshop would not be possible without the collective effort of the entire IGIB community.
Organising Head: Dr. Jitendra Narayan
For any queries regarding the workshop, materials, or access issues, please reach out:
- Email: jitendra.igib@csir.res.in
- Website: jitendralab.igib.res.in
- Event Portal: igib-events.vercel.app
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