Introduction

Panduan Hari ke-4: Hands-on Lab – 16S Amplicon Data Analysis

Hari keempat dari workshop The 9th MCC 2025 - Complete Metagenomics Hands-On Workshop with Illumina MiSeq berfokus pada analisis data amplicon 16S rRNA dari raw FASTQ hingga visualisasi komunitas mikroba. Pipeline akan mengikuti alur pada diagram: FastQC → fastp/Cutadapt → DADA2 → phyloseq (Ape, Tax4Fun2, DESeq2).

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Sesi dilaksanakan Kamis, 25 September 2025.

1) Alur Analisis

  1. Pre-processing

    • QC dengan FastQC
    • Trimming/filtering dengan Cutadapt

  2. DADA2

    • Replication count
    • Pair merge
    • Construct sequence table
    • Remove chimeras
    • Assign taxonomy
    • Evaluate accuracy

  3. Phyloseq

    • Diversity analysis
    • APE → phylogenetic tree
    • Tax4Fun2 → functional profiles
    • DESeq2 (opsional) → differential abundance

2) Minimum Requirement PC

  • CPU: minimal 4-core (≥6-core direkomendasikan).
  • RAM: minimal 8 GB (≥16 GB direkomendasikan).
  • Storage kosong: ≥20 GB.
  • OS: Linux / Windows 10/11 / macOS.

3) Tools & Paket R

Aplikasi CLI

  • FastQC → quality control.
  • fastp atau Cutadapt → trimming & filtering.
  • R (≥4.3) + RStudio

Paket R

  • dada2 → inferensi ASV
  • phyloseq → integrasi & analisis komunitas
  • ape → phylogenetic tree
  • DESeq2 → analisis diferensial abundance
  • ggplot2, pheatmap → visualisasi
  • Tax4Fun2 → prediksi fungsi mikroba

👉 Selanjutnya: Instalasi & Setup Tools

Set-up Requirement