Viromics & Phage Informatics — Hands-on

Learn how to move from raw metagenomic reads to virome and phage ecology insights. This module covers viral enrichment aware study design, assembly and vOTU calling, taxonomic and functional annotation of viruses and phages, and host linkage strategies for clinical, environmental and wastewater microbiome studies.

Viromics & Phage Informatics

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Session Index

Session 1 — Viromics Foundations & Study Design Session 2 — Viral Read QC, Assembly & vOTU Calling Session 3 — Viral Annotation, Host Linkage & Ecology Session 4 — Mini Capstone: Virome & Phage Ecology Report

Session 1

Fee: Rs 8800

Viromics Foundations & Study Design

Virome and phage ecology basics

bacteriophages, archaeal and eukaryotic viruses lytic vs lysogenic lifestyles roles in microbiome structure and AMR

Sampling and enrichment strategies for viromes

stool, wastewater, marine and soil matrices virus like particle enrichment concepts filtration and concentration considerations

Study design for virome and phage projects

controls and blanks for low biomass samples replicates and longitudinal sampling linking virome design to metagenome data

Session 2

Fee: Rs 11800

Viral Read QC, Assembly & vOTU Calling

Read QC for viromes and viral enriched data

quality trimming and adapter removal host read removal and contamination checks over amplification and low complexity reads

Assembly and detection of viral contigs

assemblers for viromes and metagenomes viral contig detection with VirSorter style tools quality and completeness of viral contigs

vOTU clustering and abundance tables

clustering viral contigs into vOTUs read mapping back to vOTUs vOTU by sample count and abundance matrices

Session 3

Fee: Rs 14800

Viral Annotation, Host Linkage & Ecology

Taxonomic and functional annotation of viral contigs

viral reference databases and vOTU catalogues protein based annotation and hallmark genes auxiliary metabolic genes and AMR cargo

Phage host prediction and linkage to microbiome data

CRISPR spacer matches and kmer approaches linking vOTUs to MAGs and taxa co abundance based host association

Virome diversity and ecological interpretation

alpha and beta diversity for vOTUs linking virome profiles to environment and disease integration with bacterial microbiome results

Session 4

Fee: Rs 18800

Mini Capstone: Virome & Phage Ecology Report

End to end virome workflow on a real dataset

theory plus guided practical

Summarising key viral and phage patterns

virome composition barplots vOTU diversity and ordination plots phage host networks and AMR related signals

Deliverables: vOTU table, linkage results and report

sample by vOTU abundance matrix R or Python analysis notebook PDF or HTML virome and phage ecology report

PDF

Viromics & Phage Informatics Training | Viral Metagenomics & Phage Ecology

Viromics & Phage Informatics — Hands-on