Pan1chr

Snakemake workflow for creating a pangenome at a chromosomic scale. Tools used within the workflow :

• PanGeTools : https://forgemia.inra.fr/alexis.mergez/pangetools
• PanGraTools : https://forgemia.inra.fr/alexis.mergez/pangratools

Place input haplotypes in data/haplotypes and reference haplotype in data/reference. By default, the reference haplotype is not included in the construction of graph. To include it, simply create a symlink to it in data/haplotypes.