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.本仓库中提交的酵母参考泛基因组图（yeast reference pangenome graphs）由Evomics实验室采用全球采样的酿酒酵母（Saccharomyces cerevisiae）菌株的高质量基因组组装结果构建而成，相关菌株数据同时涵盖于原始酿酒酵母参考组装面板（S. cerevisiae Reference Assembly Panel, ScRAP，参见O’Donnell等人2023年发表于《自然·遗传学》（Nature Genetics）的研究）及其后续扩展数据集。 各图形的详细构建规范详述如下： 1) ScRAP_v20230121_163asm.minigraph.gfa 该图形基于142个菌株的163套酵母基因组组装结果构建。简言之，我们以从酿酒酵母基因组数据库（Saccharomyces Genome Database, SGD）获取的酿酒酵母参考基因组（记为'SGDref'），以及本团队近期发布的ScRAP面板中的162套组装结果为基础，使用minigraph工具并结合命令行`minigraph -cxggs -l 5000`构建参考泛基因组图。以SGDref作为参考基因组，我们依据各酿酒酵母菌株与SGDref的系统发育距离，将其余162套其他酿酒酵母菌株的组装结果逐步添加至该图形中。随后，我们使用minigraph工具结合命令`minigraph -cxasm`将每一套输入组装结果比对至该图形，以计算对应的比对深度。