Some animations are broken. Check it.

At the IGV exercises the bam file is refered to as 'it'. This is confusing.

https://sib-swiss.github.io/NGS-introduction-training/2022.5/day2/samtools/#redirection

Some wording that is leftover from the previous version that includes filtering (e.g. the file name 11_align_sort_filter.sh)

No need to run vdb-config --interactive if using sra-tools for the first time in vscode.

polyG trimming is common for two-channel systems (like novaseq 6000). Mention this in the QC part.

Now it's based on jupyter container. Modify screenshots etc.

The directory structure during the exercises is not very clear and inconsistent. Participants run into issues while running cutadapt for the first time.

Fix or find new dataset.

Participants will be helped by a unix cheatsheet (as in the RNA-seq course)

Consider to give a different name to the bowtie2 index. Using the same name as the fasta might seem confusing at first.

At group work students are suggested to make a soft link, but this can be a bit confusing. Better to let them add the directory to the workspace.

Like lane, flow cell etc.

The word 'coverage' is used to refer to the sequencing depth of a SNP.

Add a visual slide in 'Sequencing technologies' where you see

• incorporation
• fluorescence signal
• termination

The name workdir is a bit confusing, as it looks like workspace. Also helps the participant understand that we're working in a project.

Consider making the command line exercises homework. Frees time during the course. Maybe make it a 2-day course?