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

Hands-on metagenomics: 16S and shotgun workflows, QC, host decontamination, taxonomic and functional profiling, diversity stats, assembly, binning, and reporting.

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Genomics, Transcriptomics, Molecular Systems

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
Help Desk · WhatsApp
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