You can see how the notebooks look like after being run, i.e. with all the log and graphic outputs.
- hprc_hugo24_pggb.ipynb on the construction and analysis of pangenomes with PGGB.
- RHD-RHCE - Small variant calling with Giraffe-DeepVariant.ipynb about mapping reads with Giraffe and calling small variants with DeepVariant in the RHD-RHCE region.
- pangenome-sv-genotyping.ipynb with a simple example of mapping reads with giraffe and genotyping variants.
You can also find the HTML reports and other outputs of the nf-core/pangenome Nextflow run in chrY.hprc.pan4_out, and other PDF files from the PGGB notebook.