The ScRAP yeast reference pangenome graphs (Q6034)

The yeast reference pangenome graphs deposited here are constructed by Evomics Lab using the high-quality genome assemblies of globally-sampledSaccharomyces cerevisiae strains described in both the original S. cerevisiae Reference Assembly Panel (ScRAP; See ODonnell 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 theS. 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 ODonnell 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.