LongTREC summer school

Course Description

Welcome to the LongTREC Bioinformatics Summer School on the Analysis of Long-Reads Technology Data.

We have organized a comprehensive 4-day course designed for master’s students, doctoral candidates, and early career postdoctoral fellows interested in exploring the exciting world of long-read RNA sequencing. Throughout this course, you will be introduced to a diverse range of topics — from fundamental technologies and basic data processing to advanced applications including long-read transcriptomics, single-cell analysis, and many other exciting topics.

Target Audience

This training is specifically designed for early career researchers who are:

In the grant application phase for long-read sequencing projects
Planning experimental design for studies centered around long-read technologies
Looking to expand their bioinformatics toolkit with cutting-edge long-read analysis methods

What Will You Learn?

Technologies & Fundamentals
- Comprehensive overview of different long-read sequencing technologies
- Best practices in experimental design
- Quality control evaluation using SQANTI-reads
Analysis & Applications
- Transcript identification and quantification using long reads
- Structural annotation evaluation
- Differential expression analysis and haplotype identification
- RNA modifications detection with long reads
Advanced Topics
- Single-cell and spatial transcriptomics approaches
- Principles and practical applications of metatranscriptomics

Workshop Schedule

Day 1 - 14 July 2025 | Foundation Day

Time	Session
09:00 - 12:30	Lecture: Different long-read sequencing technologies, experimental design, quality, mapping
12:30 - 13:30	Lunch Break
13:30 - 17:00	Hands-on: Different long-read mappers and QC evaluation with SQANTI-reads

Day 2 - 15 July 2025 | Transcript Analysis Day

Time	Session
09:00 - 12:30	Lecture & Hands-on: Transcript identification and quantification using long reads
12:30 - 13:30	Lunch Break
13:30 - 17:00	Lecture & Hands-on: Evaluation of structural annotation using long reads RNA sequencies

Day 3 - 16 July 2025 | Advanced Analysis Day

Time	Session
09:00 - 12:30	Lecture & Hands-on: Differential expression and haplotype analysis using long reads
12:30 - 13:30	Lunch Break
13:30 - 17:00	Lecture & Hands-on: RNA modifications with long reads

Day 4 - 17 July 2025 | Specialized Applications Day

Time	Session
09:00 - 12:30	Lecture & Hands-on: Single-cell transcriptomics with long reads
12:30 - 13:30	Lunch Break
13:30 - 17:00	Lecture & Hands-on: Metatranscriptomics with long reads