Course Identification

This course is an introduction to deep sequencing analysis. The course is based on web tools. No programming skills are required.

1. Introduction to Illumina  NGS technology
2. NGS applications and introduction to analysis
3. Illumina Primary Analysis Pipeline & Quality Control
4. Illumina library preparation
5. Sequence alignment to genome
6. RNA-Seq gene level differential expression and Mars-seq analysis
7. RNA-Seq transcript level analysis and de novo transcriptome assembly
8. RNA-Seq analysis for non-model organisms
9. Clustering analysis on gene expression data
10. Functional analysis: Gene Ontology and pathways
11. Single cell RNA-Seq technology and analysis
12. Epigenomic data analysis: ChIP-Seq & ATAC-Seq
13. Variant detection analysis
14. Long read sequencing technologies: PacBio and Nanopore
15. In-house developed NGS pipelines interface
16. Metagenomics overview

Upon successful completion of the course students will be able to:

1. Demonstrate familiarity with the common applications of deep-sequencing.
2. Discuss the basics steps of data analysis.
3. Extract the biological meaning of the results.

1.  Nature reviews: Applications of Next Generation Sequencing