Welcome to the VALT Long-read Bioinformatics Summer School.

Through this 3-day course, you will embark on the exciting journey of analyzing long-read data.

If you are a Master’s student, doctoral candidate, early career postdoctoral fellow, or just passionate about bioinformatics, this is the right course for you. With a mix of theory and hands-on exercises, you will significantly improve your knowledge and skills on the topic.

What will I learn?

• An overview of the different long-read sequencing techniques

• Best practices in experimental design

• How to create and curate a long-read defined transcriptome using SQANTI3

• Tools for the annotation of genomes using long-read transcriptomics

• How to identify and quantify transcripts

• A novel tool for the analysis of long-read single-cell data

Course pre-requisites:

To participate, you only need a laptop and familiarity with the command line. It is mandatory to have a proficiency level equivalent to completing the The Unix Shell lessons of Software Carpenter, or to work through them before the training starts.

DAY 1

• Morning Session: Lecture on different long-read sequencing technologies, experimental design, quality, and mapping.

• Afternoon Session: Hands-on training with different long-read mappers and QC evaluation using SQANTI-reads and SQANTI-browser.

DAY 2

• Morning Session: Lecture & Hands-on session for transcript identification and quantification using long reads.

• Afternoon Session: Lecture & Hands-on session on the evaluation of structural annotation using long-read RNA sequences.

DAY 3

• Morning Session: Lecture & Hands-on session covering differential expression and haplotype analysis using long reads.

• Afternoon Session: Lecture & Hands-on session focusing on single-cell transcriptomics with long reads.