OMICSS-25

Training materials for OMICSS-25 Bioinformatics Summer School

Topics

The topics are ordered in the way you should study the lectures and complete the practical sessions.
Each folder includes a README file that describes the content of that topic.

1. Bioinformatics algorithms

2. Experimental techniques

   • Sequencing
   • DNA Extraction
   • PCR,Electrophoresis

3. R

4. Linux commandline

5. NGS data analysis & file manipulation

   • FASTA/FASTQ file formats & manipulation on Linux
   • Quality Control (FASTQC, MULTIQC) & Interpretation
   • Alignment & Samtools
   • Annotation & Genomic Regions

6. Functional genomics

   • Transcriptomics (DEGs, Functional annotation)
   • Genetic variations (variant calling, IGV, GWAS)
   • Microbiome (metagenomic profiling)
   • Single-cell transcriptomics (Seurat)

7. PCA&Clustering

   • 1.PCA
   • 2.Clustering

8. Group projects

   • GP1: Machine Learning-Based Identification of Bacterial Biomarkers for Disease Classification
   • GP2: Discovery of Telomeric Biomarkers for Cancer Detection in Cell-Free DNA
   • GP3: Genomic Characterization of Population Structure in Caucasian Grape Varieties Using Whole-Genome Sequencing
   • GP4: Dissecting Lung Cancer Heterogeneity via Single-Cell Transcriptomic Profiling

SOP

1. Each topic should have its folder.
2. When creating a folder, first create it's README.md
3. Each folder should have a README with:

• The primary contributor/manager
• The contributing authors
• The description of its content
• README template:

  # Contributors
    Primary contributor: [NAME SURNAME]
    Contributing authors: [NAME SURNAME] [NAME SURNAME] [NAME SURNAME]
  # Contents  
  # TODO
    Primary contributor assigns tasks to contributing authors with deadlines

4. The following materials should be uploaded:

• Lecture slides & notes
• Exercises & tasks for practicals AND/OR notes describing the location of respective files on the server

5. Each folder can have a subfolder for separate topics. Subfolders inherit all the rules applicable to folders.
6. Commit messages should either be:

• "Complete"
• "In progress: xx%" (indicate the percentage of completeness of the overall folder or a subfolder)