• Work inside your cd /shared/team/2025_training/week2/{your_name} directory (i.e. generate output files in there

You have a Nanopore sequencing dataset in:

/shared/team/2025_training/week2/data/SRR34548621_1.fastq.gz

Try performing an in depth QC.

1. You can start using seqfu to gather read length statistics
2. You can use a new package called NanoPlot to generate QC plots for Nanopore data
   1. Check from the repository how to use it. Install it using mamba in a dedicated environment
3. If you have extra time, you can use kraken2 to profile the taxonomy
   1. Install it using mamba (in a new environment)
   2. Use this database: /shared/public/db/kraken2/pluspfp_8gb/2025-07-14/

NanoPlot example

conda create -n nanoqc -c conda-forge -c bioconda nanoplot 

NANOFILE=/shared/team/2025_training/week2/data/SRR34548621_1.fastq.gz

# Basic NanoPlot command for a single FASTQ file (using 4 threads)
NanoPlot --fastq $NANOFILE -o nanoplot_output -t 4