Setup

Create a sub-directory with your name inside week2:

cd /shared/team/2025_training/week2
mkdir andrea

This will be your working directory for this module.

Data

We have an Illumina dataset (three paired-end samples) from a human gut virome study. We also have a Nanopore sequencing of a bacterial isolate.

Inside week2 find these datasets

What we will do

1. Understand the FASTQ format
2. Identify some criteria for Quality Control of sequencing outputs
3. Perform a quality profiling of the datasets
4. Use kraken to identify contamination in the datasets
5. Understand the SAM/BAM format, and familiarise with a mapping experiment.

Some materials

• Slides on files format
• File formats tutorial