Basic Bioinformatics and Long-Read Sequencing Data Analysis

Course material for a Practical Course at the University of Bari

Software used in this course File formats used in this course

2025/12/16-20 - Introductory Module

Fundamentals of Bioinformatics and bioinformatics environment setup for DNA sequence data analysis of short read sequence data. Main genomic data formats (FASTA, FASTQ, SAM/BAM, VCF). Hands-on exercises on all topics

Day and link to lesson	Date	Topics	Preparation Required
Day 1 - shh	2025/12/16	Connection to remote machine	none
Day 1 - bash	2025/12/17	The shell	Download/install the shell
Day 2 - FastQC	2025/12/18	Assessing Read Quality	Review workshop material Setup for local machine (Option B)
Day 3 - Trimmomatic	2025/12/19	Trimming and Filtering	Review workshop material Setup for local machine (Option B)
Day 3 - Variant Calling	2025/12/19	Variant Calling Workflow	Review workshop material Setup for local machine (Option B)
Day 4 - Recap and consolidation	2026/06/06	Recap: SSH, Unix shell, FASTA/FASTQ/SAM/BAM/VCF, short-read QC, trimming, alignment, and variant calling	Review Days 1-3 lessons
Day 5 - Long reads intro and QC	2026/07/07	Long-read sequencing introduction and quality control Exercise	Review Day 4 recap
Day 6 - Long read alignment	2026/07/08	Long-read alignment Exercise	Review Day 5 lesson
Day 7 - Long-read variant calling	2026/07/10	Long-read variant calling with Clair3 and DeepVariant Exercise	Review Day 6 lesson
Extra	-	R for reproducible data analysis	Install R (latest version) Install RStudio Desktop

Advanced / Hackathon Module

Small-group project sessions for advanced students. These sessions are less prescriptive than the beginner lessons and focus on decisions, evaluation, and interpretation.

Session and link	Date	Goal	Preparation Required
7 - Advanced ONT assembly	2026/07/13	Assemble the MRSA KUN1163 genome from ONT reads and evaluate chromosome/plasmid recovery Hackathon brief	Comfortable with lessons 4-6
8 - Advanced PacBio HiFi assembly	2026/07/13	Assemble E. coli K-12 from PacBio HiFi reads and compare to reference NC_000913.3 Hackathon brief	Comfortable with lesson 7
9 - Pangenomics	2026/07/14	Build and inspect pangenome graphs with PGGB and ODGI Hackathon brief	Comfortable with lessons 7-8
10 - Pangenomics variant calling	2026/07/15	Use VG Giraffe read mapping and graph-based variant calling Hackathon brief	Complete lesson 9
11 - Pangenomics genotyping	2026/07/16	Follow the PanGenie workshop for pangenome-based genotyping Hackathon brief	Complete lesson 10

Acknowledgments

This course material includes content adapted from Software Carpentry lessons, which are made available under the Creative Commons Attribution license (CC BY 4.0).

The sections listed above incorporate or adapt Software Carpentry materials.