Syllabus

Week 1 (23.09.2025)

• Intro to practical course. Strategy of analysis

• HW: install WSL, learning basic shell commands, make HW1_shell_commands task

• Presentation - Google Slides

Week 2 (30.09.2025)

• Sanger Sequencing. Design of primers for Sanger Sequencing. SnapGene

• HW: Install SnapGene Viewer. Make HW2_SnapGene task.

• Presentation - Google Slides

Week 3-4(07.10.2025-14.10.2025)

• NGS analysis part 1. Library preparation, sample quality assessment, QC of reads(fastQC/multiQC)

• HW: Ecoli_Genome_Assembly_Part_1

• Presentation: Google Slides, DNA Purification&QC

Week 5(21.10.2025)

• NGS analysis part 2. Mapping reads to reference genome. SAM/BAM files. De novo assembly.
• Presentation: Google Slides
• Test1

Week 6(28.10.2025)

• NGS analysis part 3. Variant calling. VCF files. Annotation of variants
• HW: Ecoli_Genome_Assembly_Part_2
• Presentation: Google Slides

Week 7(04.11.2025)

• Types of Genetic Polymorphisms. SNPs, Indels, CNVs, Structural Variants
• HW:
• Presentation:

Week 8(11.11.2025)

• Analysis of annotated VCF files.VEP.Fst.Tadjima’s D.
• HW:
• Presentation:

Week 9(18.11.2025)

• Oxford Nanopore sequencing. Long reads. Applications.
• HW:
• Presentation:

Week 10(25.11.2025)

• R in genomics
• HW:
• Presentation:

Week 11(02.12.2025)

• Guest Lecture

Week 12(09.12.2025)

• Presentation group’s results. Summary of the course
• Template of presentation - Google Slides