Functional Profiling & Pathway Reconstruction — Hands-on

Learn how to turn shotgun metagenomics reads into interpretable functional profiles and pathways. This module focuses on gene family abundance (KOs, ECs, UniRef) , HUMAnN-style workflows, KEGG/MetaCyc pathway reconstruction, normalization strategies, and differential functional analysis in microbiome and AMR contexts.

Functional Profiling & Pathway Reconstruction

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Session Index

Session 1 — Functional Profiling Concepts & Gene Families Session 2 — HUMAnN Workflows & Pathway Reconstruction Session 3 — Normalization & Differential Functional Analysis Session 4 — Mini Capstone: Taxon-to-Function Story

Session 1

Fee: Rs 8800

Functional Profiling Concepts & Gene Families

From taxonomic to functional views of microbiomes

genes, pathways and modules taxon contribution to function context for AMR and metabolism

Gene family concepts and annotation spaces

KEGG Orthology (KOs) , EC numbers UniRef90/50, eggNOG, COGs GO terms and functional categories

Read alignment and translated search basics

pangenome and protein databases Bowtie2 / DIAMOND style workflows sensitivity vs runtime trade offs

Session 2

Fee: Rs 11800

HUMAnN Workflows & Pathway Reconstruction

HUMAnN style pipelines: overview and logic

taxonomic prescreening pangenome versus unaligned reads gene families to pathways

Pathway reconstruction with KEGG/MetaCyc style resources

pathway definitions and modules presence/absence vs abundance completeness thresholds

Outputs: gene family, pathway and contribution tables

stratified vs unstratified outputs linking to taxonomic profiles export for R and Python analysis

Session 3

Fee: Rs 14800

Normalization & Differential Functional Analysis

Units, scaling and compositionality in functional data

RPK, RPKM, CPM and relative abundance copies per million vs coverage link to compositional thinking

Normalization and transformation strategies

library size and length corrections CLR/log transforms for functions batch and covariate adjustment overview

Differential pathway and gene family analysis

DESeq2 / edgeR style workflows multiple testing and effect sizes visualizations: volcano, heatmaps

Session 4

Fee: Rs 18800

Mini Capstone: Taxon-to-Function Story

Designing a small functional profiling analysis

guided theory plus practical

Running a HUMAnN style workflow on a teaching dataset

gene family and pathway tables basic differential functions link to taxon profiles from earlier modules

Deliverables: figures, tables and narrative for a microbiome question

functional heatmaps and barplots pathway summary tables short report tying taxa to functions

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Functional Profiling & Pathway Reconstruction Training | HUMAnN, KEGG/MetaCyc & Differential Functions

Functional Profiling & Pathway Reconstruction — Hands-on