Are you eager to master Next-Generation Sequencing (NGS) and unlock the secrets of the Genome? Join our specialized 6-Month Internship Program designed to take you from Linux command-line basics to advanced Metagenomics and Whole Genome Assembly.

📚 Course Curriculum & Modules: This internship covers 24+12 (project) classes divided into 10 intensive modules, including a dedicated 3-month research project.

Module 1: Foundations of Bioinformatics & Linux Environment
Kickstart your journey by mastering the essential environment for genomic analysis. In this module, you will understand the intricacies of Genome Sequencing technologies and file formats (FASTQ, BAM, VCF). You will transition to a professional setup by mastering the Linux Command Line (Ubuntu/WSL) and learning to manage packages using Conda/Bioconda.

Module 2: Quality Control & Pre-processing (Universal) 
Data quality is the backbone of reliable research. You will learn to assess raw sequencing data using FastQC and aggregate reports with MultiQC. This module focuses on rigorous data cleaning—removing adapters and trimming low-quality bases using tools like Trimmomatic and Cutadapt to ensure your data is ready for analysis.

Module 3: Reference-Based Mapping & Variant Calling
Dive into the core NGS workflow. You will learn to map reads to a reference genome using BWA and manage alignment files with Samtools. The module focuses on identifying genetic variations (SNPs & Indels) using GATK HaplotypeCaller, followed by the visual inspection of variants using the IGV browser.

Module 4: Bacterial Genome Assembly & Annotation 
Master the art of assembling microbial genomes. You will use SPAdes for de novo assembly and evaluate the quality using QUAST. This module goes beyond basics by teaching you to annotate genes with Prokka, identify Antibiotic Resistance (AMR) genes, and perform comprehensive Pan-Genome Analysis to study bacterial evolution.

Module 5: Animal Genome Assembly & Annotation 
Scale up your skills to handle complex eukaryotic genomes. You will learn strategies for chromosome-level scaffolding and handling repetitive regions. The module covers advanced structural annotation using pipelines like BRAKER/MAKER and repeat masking to distinguish between Exons, Introns, and UTRs.

Module 6: Metagenomics Part 1: Amplicon (16S rRNA)
Explore microbial communities without culturing them. This module introduces the QIIME2 ecosystem for 16S rRNA analysis. You will learn to generate ASVs using DADA2, assign taxonomy using Naive Bayes classifiers, and visualize community diversity through Alpha and Beta diversity plots.

Module 7: Metagenomics Part 2: Shotgun (Assembly & Binning) 
Advance to Whole Genome Shotgun (WGS) metagenomics. Learn to remove host (human) DNA contamination and perform meta-assembly using MegaHIT. The highlight of this module is Genome Binning—reconstructing individual genomes (MAGs) from complex microbial communities and assessing their quality using dRep.

Module 8: Taxonomic Assignments & Functional Metagenomics
Go beyond "who is there" to "what are they doing." You will place your Metagenome-Assembled Genomes (MAGs) into the tree of life and perform functional annotation using COG and KEGG databases. Learn to reconstruct metabolic pathways and identify community-wide antibiotic resistance.

Module 9: Applied Microbiome Analysis (Human, Animal & Environment) 
Apply your knowledge to real-world scenarios under the "One Health" concept. This module covers the analysis of Host-Associated microbiomes (Human Gut, Livestock) and Environmental microbiomes (Soil, Marine). You will explore dysbiosis, pathogen transmission, and AMR surveillance across clinical and environmental sectors.

Module 10: Research Project & Career Guidelines Classes 25 - 36 (3 Months) 
Apply your skills in a real-world scenario. The final three months are dedicated to a specialized research project in either NGS or Metagenomics. Under expert mentorship, you will select a topic, conduct research, and learn the step-by-step process of Scientific Paper Writing, preparing you for publication and a career in research.