Strain Level Resolution & SNV Dynamics — Hands-on

Learn how to go beyond species level microbiome summaries and characterize strains and within species diversity. You will configure mapping and SNV calling workflows, build haplotype level views, quantify microdiversity and design strain tracking analyses for clinical, environmental and transmission focused projects.

Strain Level Resolution and SNV Dynamics

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Session Index

Session 1 — Strain Concepts, Microdiversity & Study Design Session 2 — Mapping, SNV Calling & Filtering Session 3 — Strain Tracking, Haplotypes & Dynamics Session 4 — Mini Capstone: Strain Dynamics Report

Session 1

Fee: Rs 8800

Strain Concepts, Microdiversity & Study Design

Strain level vs species level microbiome views

clonal vs mixed populations within host and between host diversity links to function and phenotype

Microdiversity and SNV level thinking

SNVs vs gene content differences allele frequencies and mixtures selection vs drift perspectives

Study design for strain resolution projects

depth and coverage requirements longitudinal vs cross sectional host and environmental metadata

Session 2

Fee: Rs 11800

Mapping, SNV Calling & Filtering

Read mapping strategies for strain analysis

mapping to reference genomes or MAGs multi mapping and ambiguous reads coverage uniformity checks

SNV calling in metagenomic contexts

variant callers and parameters allele frequency and depth filters handling low frequency variants

Filtering, masking and QC of SNV sets

masking low complexity regions removing unreliable sites building high confidence variant tables

Session 3

Fee: Rs 14800

Strain Tracking, Haplotypes & Dynamics

Haplotype and strain reconstruction concepts

linkage of SNVs across reads dominant vs minor strains uncertainty in haplotype assignments

Strain tracking across hosts, sites and time

distance metrics between samples relatedness and transmission thinking gain and loss of strains over time

Microdiversity summaries and visualizations

site frequency spectra per gene and genome level views sample wise microdiversity indexes

Session 4

Fee: Rs 18800

Mini Capstone: Strain Dynamics Report

End to end SNV and strain workflow on a cohort

Theory plus guided practical

Interpreting strain changes with metadata and outcomes

linking strain shifts to interventions clinical and environmental examples caveats and limitations for decision making

Deliverables: SNV tables, plots and methods block

high confidence SNV and strain tables microdiversity and tracking figures ready to reuse methods and parameters

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Strain Level Resolution & SNV Dynamics Training | Strain Tracking & Microdiversity

Strain Level Resolution & SNV Dynamics — Hands-on