A Hands-On Program for Genomic Data Analysis

1. Week 1: Introduction to Genomics and Data Types

   • Basics of genome organization and sequencing technologies

   • NGS platforms: Illumina, Oxford Nanopore, PacBio

   • Types of genomic data: FASTQ, BAM, VCF, GFF

   • Introduction to Linux and command-line interfaces for bioinformatics

   Week 2: Sequence Data Quality Control and Alignment

   • Quality assessment using FastQC and trimming tools (Trimmomatic, Cutadapt)

   • Genome indexing and alignment using BWA/Bowtie2

   • File conversions and manipulations using SAMtools

   • Hands-on exercises with reference genome and raw data

   Week 3: Variant Calling, Annotation, and Interpretation

   • SNP and Indel calling with GATK, FreeBayes

   • Functional annotation using ANNOVAR and SnpEff

   • Integrating variant data with databases (ClinVar, dbSNP, gnomAD)

   • Interpreting disease-associated mutations and population variation

   Week 4: Transcriptomics and Advanced Analytical Workflows

   • RNA-Seq data processing and differential gene expression (DESeq2, edgeR)

   • Visualization tools: IGV, UCSC Genome Browser, heatmaps, PCA

   • Functional enrichment: GO, KEGG, Reactome

   • Introduction to machine learning in genomic data classification

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• Enhanced understanding of genomic data analysis techniques.
• Practical experience with bioinformatics tools.
• Improved data visualization and interpretation skills.
• Familiarity with current trends in genomics research.
• A foundational knowledge base for further studies in bioinformatics.