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ONE HEALTH · PATHOGEN GENOMICS

BIOINFORMATICS FOR One Health

Five-Day Hands-on Workshop
Pathogen Genomics, Metagenomics & Antimicrobial Resistance Surveillance

Dates

Mar 16-20, 2026

Location

CSIR-IGIB, Delhi

Mode

In-person

Data RepoHPC Cockpit

Organized by:

Jitendra Lab of Bioinformatics and Big Data at

CSIR- Institute of Genomics and Integrative Biology (CSIR-IGIB)

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Unlock the power of genomic data through our comprehensive, day-by-day training modules and specialized resources.

Day 1
Day 1: The Genomic Compass

Navigating One Health Bioinformatics

Setting up computational environments and mastering the command line—the backbone of bioinformatics.

Today's Focus

Installation and Linux system setup
Command-line navigation and Unix utilities (grep, awk, sed)
BASH scripting and environment management with Conda/Mamba
LinuxBashCondaGitseqkitseqtk
Access Repository
Star the repo to support our community!
Linux Basics & IntroductionSandbox.bio
Day 2
Day 2: The Assembly Quest

From Raw Data to Complete Genomes

Transforming fragmented sequencing data into contiguous genome representations through computational reconstruction.

Today's Focus

Understanding De-novo assembly workflows
Performing assembly quality assessment (QA)
Reference-based vs De-novo assembly comparisons
SPAdesFlyeCanuQUASTMinimap2
Access Repository
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Genome Assembly ConceptsAssembly Quality & ImprovementQUAST Tool
Day 3
Day 3: Pathogen Surveillance

AMR & Virulence Prediction

Master practical detection of resistance genes and virulence factors using state-of-the-art bioinformatics tools.

Today's Focus

Exploring AMR databases (CARD, ResFinder)
Genome-based resistance tool workflows
Interpreting AMR dynamics in clinical and research settings
AMRFinderPlusRGIABRicateCARDNexus
Access Repository
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AMR & Virulence PredictionAMR: Genomic PerspectiveAMRFinderPlusAMR India Nexus
Day 4
Day 4: Evolution & Alignment

Sequence Comparison & Mutational Hotspots

Analyzing simple sequence repeats (SSRs) and evolutionary patterns across multiple genomes.

Today's Focus

Advanced sequence alignment scoring models
SSR mediated adaptive genome evolution
Identifying mutational hotspots in genomic data
croSSRoadClustalWMAFFTMUSCLE
Access Repository
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Sequence Alignment GuideScoring DNA/Protein AlignmentcroSSRoad SSR DatabaseMultiple Sequence AlignmentcroSSRoad Tool

Key References

croSSRoad GitHub
Day 5
Day 5: Advanced Resources

Specialized Tools & Knowledgebases

Harnessing integrated, curated knowledgebases for deep genomic insights and target drug discovery.

Today's Focus

Integrated resources for WHO priority pathogens
Functional enrichment and genome annotation
AI-driven prediction of antimicrobial resistance
ARKbaseSPARAGetEnrichChitra
Access Repository
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Specialized Genomic ResourcesChitra PresentationARKbase 1.0GetEnrichChitra ToolSPARA ML

Key References

ARKbase NAR 2024GetEnrich Paper
Foundation
NGS File Formats & Tools

Essential grounding in the various file formats used in NGS and installation of required bioinformatics tools.

FASTQSAM/BAMVCFGFFTrimmomaticFastQCMultiQC
Essential NGS FormatsTools Installation WorkshopMultiQC Paper

Join Our Open Source Community

All our workshop materials, scripts, and tutorials are open source. Help us grow the community by starring our repositories on GitHub!

Star the Main Repo 🥲
5-Day Program

Workshop Schedule

Comprehensive 5-day program with lectures and hands-on training

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🚀 Quick Access Links

Workshop Participants: Click here to log in to your pre-configured HPC server environments for the hands-on sessions.

HPC Resource Cockpit

Contact & Resources

Access workshop materials and get in touch with organizers

Get in Touch

CSIR-IGIB Email

jitendra.igib@csir.res.in

BioinformaticsOnLine

info@bioinformaticsonline.com

Phone

+91 7835999528

Venue

CSIR- Institute of Genomics and Integrative Biology
Mathura Road Campus
Delhi, India

Visit CSIR-IGIB Website

Workshop Resources

Resource Cockpit

Access for registered users

Download Brochure

Workshop details & information

View Full Schedule

Complete 5-day program

Hands-on Sessions

Google Colab notebooks

Sandbox.bio

Interactive browser-based tutorials

About CSIR-IGIB

The CSIR-Institute of Genomics and Integrative Biology is a premier research institute dedicated to advancing genomics and integrative biology research. The institute focuses on translational research in genomics, molecular medicine, and bioinformatics.

Organized by: CSIR-IGIB•Funded by: Skill India Project (IGIB: HCP002502/2025/E-I)
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Partners & Affiliations

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A Skill India project by CSIR-IGIB

Crafted with ❤️ in Jitendra Lab by
PP & 😅 Robot AI

© 2026 CSIR-Institute of Genomics and Integrative Biology. All rights reserved.

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