Advancing One Health through Genomics Data & Discovery. Comprehensive training in pathogen genomics, metagenomics, and antimicrobial resistance surveillance.
Dates
Nov 3-7, 2025
Venue
CSIR-IGIB
Format
In-person
Organized by:
CSIR- Institute of Genomics and Integrative Biology (CSIR-IGIB)
Funded by: Indian Council of Medical Research (ICMR)
Comprehensive practical training from Linux basics to advanced genomics analysis
Tools:
Objective:
Learn essential terminal operations, environment setup, and basic automation to support downstream analysis.
Install:
mamba install -c bioconda bash coreutilsTools:
Objective:
Perform data quality control to ensure accurate downstream genome assembly.
Install:
mamba install -c bioconda fastqc trimmomatic multiqcTools:
Objective:
Assemble raw reads into contigs and scaffolds for metagenomic datasets.
Install:
mamba install -c bioconda spadesTools:
Objective:
Assess assembly completeness and extract representative genomes.
Install:
mamba install -c bioconda quast metabat2Tools:
Objective:
Characterize microbial community composition and metabolic potential from metagenomic data.
Install:
mamba install -c bioconda kraken2 krona metaphlan humannTools:
Objective:
Predict antimicrobial resistance and virulence factors from genome sequences.
Install:
mamba install -c bioconda ncbi-amrfinderplusTools:
Objective:
Use artificial intelligence to predict AMR and microbial function from hologenomic data.
Install:
pip install spara-mlTools:
Objective:
Annotate bacterial genomes and interpret gene functions through pathway analysis.
Install:
mamba install -c bioconda prokkaTools:
Objective:
Compare multiple genomes to identify conserved and unique genes, chromosomal breakpoints, and genome rearrangements.
Install:
mamba install -c bioconda roaryTools:
Objective:
Construct complete pathogen genomes and compare reference-based and de-novo assemblies.
Install:
mamba install -c bioconda minimap2 bwa samtools bcftools flye canu spadesTools:
Objective:
Analyze host transcriptional changes during infection and visualize gene interaction networks.
Install:
mamba install -c bioconda bioconductor-deseq2 bioconductor-limma r-ggplot2Access all workshop sample datasets in one central location. This Google Drive folder contains data for all training sessions.
Workshop materials are available on Tejas HPC. Access via the Resource Cockpit using the path below:
/home/workshop/Learn from leading experts in genomics, AI, and bioinformatics
Principal Scientist
CSIR-IGIBBioinformatics, Genome Evolution, Chromosome Breakpoints, Comparative Genomics. Expert in big data and informatics, bacterial and archaeal genomics, evolutionary genomics, metagenomics, and structural genomics.
Session:
Genome Assembly (Tuesday, Nov 4 - 9:30 AM)
Associate Professor
BRIC-National Institute of Biomedical GenomicsHuman Metagenomics, Population Genomics, Molecular Biology. Specializes in host-microbiome interactions in human health and disease, with focus on Psoriasis, Atopic Dermatitis, and Colorectal Cancer.
Session:
Precision Microbiomics: Unraveling the Antimicrobial Resistome (Tuesday, Nov 4 - 12:00 PM)
Chief Scientist
CSIR-IGIBMetagenomics, Microbial Diversity, Metal-Microbe Interactions. Focuses on microbial diversity and function using metagenomics, exploiting the microbiome for novel bioactive molecules.
Session:
Microbial Diversity, Pathogens and AMR of Waterbodies (Tuesday, Nov 4 - 3:30 PM)
Professor of Bioinformatics
SCIS, Jawaharlal Nehru UniversityAI/ML methods for Bioinformatics, Protein-DNA Structural Interactions. Leads SciWhyLab developing data-driven algorithms using machine learning, deep learning, and big data analytics.
Session:
NGS Data Analysis using AI Methods (Wednesday, Nov 5 - 9:30 AM)
Principal Scientist
CSIR-IGIBIntegrative Genomics of Host-Pathogen, Single Cell Multiomics, Co-infections. Notable work on SARS-CoV-2 research with 1385+ citations on Delta variant studies.
Session:
Economics of Genomics: Active and Inactive Microbes (Wednesday, Nov 5 - 11:30 AM)
Professor
University of DelhiMulti-omic investigation of microbial resistance mechanisms, Bioinformatics, Chemi-informatics, Phylogenomics. Specializes in analysis of microbial genomes and structure-based drug designing.
Session:
Discovery of Drug Resistance Factors in Multi-Omics Data (Wednesday, Nov 5 - 2:00 PM)
Principal Scientist
CSIR-IGIBMedical Informatics, Computational Biology, Next Generation Sequencing, Personalized Medicine, Machine Learning. Leads Digital and Genomic Medicine lab with notable publication on deep learning-based multi-omics integration (965 citations).
Session:
Federated AI for Longitudinal Surveillance of AMR (Thursday, Nov 6 - 9:30 AM)
Scientist
Indian Biological Data Centre (IBDC)Nucleotide Archival Services, GenomeIndia initiative, INSACOG, NGS Analysis. Manages national biological data infrastructure, including nucleotide data archive portals (INDA, INSACOG, Genome India).
Session:
Integrating Data and Discovery: IBDC for Pathogen Research (Friday, Nov 7 - 9:30 AM)
Principal Scientist
CSIR-IGIBStructural Biology, X-ray Crystallography, Genome Informatics. Expert in mycobacterial proteins and structural analysis of genome components.
Session:
Team Member
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The global health landscape is increasingly challenged by the rapid emergence of infectious diseases (EIDs) and the escalating threat of antimicrobial resistance (AMR). This workshop champions the "One Health" philosophy, recognizing the inextricable link between the health of humans, animals, and our shared environment.
Building expertise for the future of pathogen surveillance and bioinformatics
Provide participants with foundational knowledge in bioinformatics applied to emerging infectious diseases and antimicrobial resistance.
Introduce key genomic sequencing technologies and their applications in public health.
Train participants in the practical use of bioinformatics tools for genomic data analysis.
Enable participants to interpret genomic data for informed public health decision-making.
Foster a collaborative network among researchers working on One Health initiatives and bioinformatics.
Enhance local capacity for genomic surveillance and outbreak response using advanced bioinformatics techniques.
View the complete digital standee with detailed schedules, team members, and workshop highlights
View Digital StandeeAccess workshop materials and get in touch with organizers
CSIR-IGIB Email
jitendra.igib@csir.res.inBioinformaticsOnLine
info@bioinformaticsonline.comPhone
+91 7835999528Venue
CSIR- Institute of Genomics and Integrative Biology
Mathura Road Campus
Delhi, India
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.