Module 1

Foundations of Microbiome Sequencing and Amplicon Analysis

Week 1: Targeted Amplicon Sequencing

• Introduction to UNIX, environment management with conda.

• Experimental design consideration

• Tool focus: fastp, fastqc, multiqc, writing shell script

Week 2: Amplicon Seq Analysis 

• OTU vs. ASV, Decontamination, databases 

• Tool focus: decontam, DADA2

Week 3: Diversity and composition analysis

• Alpha/Beta diversity, Rarefaction, PCoA, PERMANOVA, CLR, ANCOM-BC2, differential abundance

• Tool focus: PhyloSeq, PICRUSt2

Module 2

Shotgun Metagenomics, Genome Reconstruction, and Functional Annotation

Week 4: Introduction to shotgun metagenomics

• K-mer, Hash, ANI based approaches

• Tool focus: Kraken2/Bracken, SourMash, Sylph, MetaPhlAn2

Week 5: Metagenome assembly

• Short-, long-read, and hybrid assembly methods

• Tool focus: Flye, Spades, Bandage

• R analysis: ANCOV vs. DESeq2

Week 6: Binning and Metagenome-Assembled Genomes (MAG)

• Functional annotation, GO enrichment, KEGG, EC, Pfam

• Tool focus: Tool focus: MetaBAT, MaxBin, CheckM2, DRAM, BAKTA, egg-nog mapper

Module 3

Advanced Metagenomics Applications and Independent Research Project

Week 7: Ressistome analysis

• ARG and time series analysis

• Biomarker discovery

• Tool focus: RGI (CARD), LefSE

Week 8: Mobilome analysis

• Detecting phage and plasmids

• Tool focus: MOB-suite, geNomad, CheckV

• Final projects overview: four tracks of a metagenomics project (read-based profiling, assembly and MAG-profiling, resistome and MGE analysis, temporal and statistical analysis)

Week 9-12: Final project and extended support

• The instructor will provide project ideas and case studies.

• Students will conduct independent final projects.

• Extended support.

Blogs By the Instructor

Python For Bioinformatics: https://arftrhmn.net/python-for-bioinformatics/

Microbial ortholog gene clustering using real-dataset: https://arftrhmn.net/microbial-ortholog-gene-clustering-using-real-dataset/

Microbial De Novo Genome Assembly from Short-Read Data: https://arftrhmn.net/microbial-genome-assembly-workflow-for-short-read-data/

Creating a Publication Quality Phylogeny Using ggtree: https://arftrhmn.net/creating-a-publication-quality-phylogeny-using-ggtree/  

বায়োইনফরমেটিক্স শিখতে আমি যে পাঁচটি বই পড়েছি: https://arftrhmn.net/books_for_learning_bioinformatics/