全基因组参考通过存储一组代表性的不同单倍型及其比对（通常以图表的形式）来解决参考基因组的偏差。由变异调用者确定的替代等位基因可用于构建泛基因组图，但长读长测序的进步正在导致广泛可用的高质量定相组装。与变体调用相反，直接从程序集构建泛基因组图，利用了图表示不同尺度变异的能力。在这里，我们展示了 Minigraph-Cactus 泛基因组管道，该管道直接根据全基因组比对创建泛基因组，并展示了其扩展到人类泛基因组参考联盟的 90 种人类单倍型的能力。该方法构建包含所有形式的遗传变异的图表，同时允许使用当前的绘图和基因分型工具。我们测量了用于泛基因组内分析的参考基因组的质量和完整性的影响，并表明使用来自端粒到端粒联盟的 CHM13 参考可以提高我们方法的准确性。我们还展示了果蝇全基因组的构建。

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Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph’s ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.