Course material for a Practical Course at the University of Bari
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) |
| Extra | - | R for reproducible data analysis | Install R (latest version) Install RStudio Desktop |
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.