The ScRAP yeast reference pangenome graphs

The yeast reference pangenome graphs deposited here are constructed by Evomics Lab using the high-quality genome assemblies of globally-sampled Saccharomyces cerevisiae strains described in both the original S. cerevisiae Reference Assembly Panel (ScRAP; See O’Donnell et al. Nature Genetics, 2023) and its future extensions. 

The detailed construction specification for each graphs are described below:

1) ScRAP_v20230121_163asm.minigraph.gfa

This graph was built upon 163 yeast genome assemblies from 142 strains. Briefly, we took the S. cerevisiae reference genome (denoted as 'SGDref') retrieved from the Saccharomyces genome database (SGD) as well as 162 assemblies from our recently released S. cerevisiae Reference Assembly Panel (ScRAP; See O’Donnell et al. Nature Genetics, 2023) to construct reference pangenome graph by using minigraph with the command ‘minigraph -cxggs -l 5000’. With the SGDref as the reference genome, we incrementally added those 162 assemblies of other S. cerevisiae strains into the graph according to their phylogenetic distances to SGDref. We further mapped each input assembly to the graph by minigraph with the command ‘minigraph -cxasm’ to calculate the corresponding mapping depth.