The Genomics Laboratory served as a dedicated facility supporting genomic, microbiome, metagenomic, and molecular research during the reporting period. It provided end-to-end technical support spanning biological sample processing, nucleic acid extraction, quality assessment, sequencing library preparation, next-generation sequencing, sequencing quality control, bioinformatics analysis, and data interpretation.

Over the reporting period, the laboratory processed 136 samples and conducted 10 sequencing runs across 61.73 Gb of generated data, supporting 3 research projects that used 16S rRNA, full-length 16S, metagenomic, and/or whole-genome sequencing approaches. It also delivered on-site training in genomic laboratory techniques, sequencing, and bioinformatics, giving undergraduate students, research scholars, and faculty direct, hands-on exposure to modern genomics workflows. Overall, the laboratory meaningfully strengthened institutional capacity in genomic research, sequencing-based analysis, and hands-on student skill development.

The major objectives of the Genomics Laboratory during the reporting period were to

• Provide undergraduate students in microbiology and computer science at the college with hands-on experience and skill development in next-generation sequencing, genomics, metagenomics, and related areas.
• Foster research in fields such as metagenomics, genomics, and transcriptomics for B.Sc. (Hons) Microbiology dissertations.
• Offer training opportunities to students and faculty from other colleges (on chargeable basis) of University of Delhi and other universities.
• Provide research support to PhD students specializing in genomics, metagenomics and meta-transcriptomics registered under the RLA faculty.
• Offering sequencing and analysis services on chargeable basis to research groups

The laboratory conducted sequencing activities using Oxford Nanopore Technology (ONT)-based workflows. The workflow included library preparation, native barcoding where required, flow-cell preparation, sequencing, run monitoring, and post- run quality assessment. In total, 10 sequencing runs were conducted, covering 136 samples.

The centre also supported downstream processing and analysis of sequencing data, using a standardized computational workflow for quality assessment, preprocessing, taxonomic classification, metagenomic analysis, and statistical interpretation, tailored to individual project objectives. Major bioinformatics activities included

• Basecalling and sequencing quality assessment
• Read filtering and quality control
• Host-read removal
• Taxonomic classification and abundance estimation
• Metagenomic assembly and functional annotation
• Antimicrobial resistance gene (resistome) analysis
• Virulence-factor analysis
• Heavy-metal resistance gene analysis
• Plastic-degrading gene analysis
• Alpha and beta diversity analysis
• Differential abundance and statistical analysis
• Data visualization, interpretation, and reporting

Where applicable, analysis was performed using Epi2me, Dorado, NanoPlot, Porechop, Filtlong, Kraken2, Bracken, Flye, R, phyloseq, DESeq2, LEfSe, and relevant genomic and microbial databases

A central goal of the Genomics Laboratory is to build genomics and bioinformatics capacity among students, not only through instruction but through direct, supervised participation in live sequencing work. The laboratory organized an on-site training programme for undergraduate students and researchers to build practical understanding of genomic laboratory workflows and sequencing technologies, combining demonstrations with hands-on sessions.

Student Training Opportunities — At a Glance

• Hands-on training on next-generation sequencing (Oxford Nanopore workflows), from sample processing through data interpretation by personnel from ONT.
• Structured, dedicated training modules developed on Nanopore sequencing, developed specifically for the programme.
• Practical experience across the full laboratory pipeline: DNA extraction, quantification and quality assessment, PCR-based workflows, and library preparation.
• Direct operation of sequencing instruments — flow-cell handling, sequencing run set-up and monitoring, and sequencing quality control.
• Introductory bioinformatics training, including interpretation of sequencing results, giving students a first grounding in computational genomics.
• Research-linked training pathways: 7 UG dissertations and research projects supported, giving Microbiology undergraduates a route from classroom training into independent project work.
• research support to PhD scholars working in genomics, and metagenomics.

Training sessions covered the full pipeline students would encounter in a real sequencing project: sample processing and handling, DNA extraction, DNA quantification and quality assessment, PCR-based workflows, library preparation, the Nanopore sequencing workflow, flow-cell handling, sequencing run set-up and monitoring, sequencing quality control, basic bioinformatics, and interpretation of sequencing results. Because these sessions used live samples and functioning instruments rather than simulations, participating students gained direct, transferable laboratory skills rather than only theoretical exposure.

Dr. Gunjan Sharma was appointed as Scientist Level-I (14/07/2025 – 31/10/2025) to support the Genomics Laboratory's activities. In this role, she supported routine operations, sequencing, data management, documentation, and troubleshooting, and prepared the training modules used for Nanopore sequencing instruction.

• Successful implementation of genomic and sequencing workflows within the laboratory.
• Completion of 10 sequencing runs involving 136 samples.
• Generation of approximately 61.73 Gb of sequencing data.
• Successful support of 3 research projects and 4 UG dissertations.
• Offered sequencing and analysis services for 10 samples on chargeable basis to a research group
• Establishment and optimization of DNA extraction and library preparation workflows.
• Implementation of sequencing quality-control procedures.
• Development and application of bioinformatics workflows for genomic data analysis.
• Delivery of on-site DNA sequencing training to research scholars, faculty, and undergraduate students, giving participants direct experience with metagenomic workflows.
• Strengthening of technical capacity through hands-on training and knowledge transfer.
• Appointment and engagement of dedicated technical personnel for routine laboratory operations.
• Improvement of laboratory documentation, sample tracking, and sequencing data management.
• Strengthening of institutional capacity for future genomic and metagenomic research.