Metagenomics & Microbiome Informatics — Hands-on

Gain expertise in 16S and shotgun metagenomics—QC, host decontamination, taxonomic and functional profiling, diversity statistics, assembly, binning, and reproducible reporting.

Metagenomics & Microbiome Informatics

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Session Index

Session 1 — Design, QC & Decontamination Session 2 — Taxonomy & Diversity Analytics Session 3 — Functional Profiling, Assembly & Binning Session 4 — Mini Capstone: Microbiome Pipeline

Session 1

Fee: Rs 6300

Design, QC & Decontamination

Study design for 16S vs shotgun; controls and metadata schemas

Theory

Read QC, trimming and adapter removal; human host depletion

FastQC MultiQC fastp Trimmomatic KneadData Bowtie2

rRNA amplicon denoising vs shotgun mapping concepts

QIIME 2 DADA2 Deblur

Session 2

Fee: Rs 8400

Taxonomy & Diversity Analytics

Taxonomic profiling and reference databases

Kraken2/Bracken MetaPhlAn SILVA/Greengenes

Alpha/beta diversity, ordination and hypothesis testing

Shannon/Simpson Bray–Curtis/UniFrac PCoA/NMDS PERMANOVA

Visualization and reporting layers

phyloseq ggplot2 plotly

Session 3

Fee: Rs 11200

Functional Profiling, Assembly & Binning

Pathways and gene families from shotgun data

HUMAnN UniRef KEGG/eggNOG

De novo assembly, binning and MAG quality checks

MEGAHIT/metaSPAdes MetaBAT2/MaxBin2/CONCOCT CheckM/GTDB-Tk

Resistance and virulence screens (optional)

CARD ResFinder VFDB

Session 4

Fee: Rs 14000

Mini Capstone: Microbiome Pipeline

Design an end to end 16S or shotgun pipeline with provenance

Theory

Automate ingest→QC→taxa→function→report with dashboards

Snakemake Conda/Mamba Quarto/JupyterLab

Export figures, biom/tables and submission-ready metadata

QIIME 2 BIOM ENA/GEO/SRA

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Metagenomics & Microbiome Informatics Training | QIIME 2, Kraken2/Bracken, HUMAnN, Assembly & Binning

Metagenomics & Microbiome Informatics — Hands-on