加州大学团队发表利用Minigraph-Cactus基因组比对构建了泛基因组图谱

《自然-生物技术》杂志发表了美国加州大学Benedict Paten和Glenn Hickey共同合作的科研成果：
利用Minigraph-Cactus基因组比对构建了泛基因组图谱。
该研究团队展示了Minigraph-Cactus泛基因组工具，
它直接从全基因组比对中创建泛基因组，
并展示了它扩展到来自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遗传变异的图表，同时允许使用当前的图谱绘制和基因分型工具。
研究人员测量了用于泛基因组分析的参考基因组的质量和完整性的影响，
并表明使用端粒到端粒联盟的CHM13参考可以提高这一方法的准确性。



Title
Pangenome graph construction from genome alignments with Minigraph-Cactus

Author
Hickey, Glenn, Monlong, Jean, Ebler, Jana, Novak, Adam M.,
Eizenga, Jordan M., Gao, Yan, Marschall, Tobias, Li, Heng, Paten, Benedict

Issue&Volume
2023-05-10

Abstract

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.

杭州图博基因科技有限公司，专注于基因数据库建设、DNA数据库建设、eccDNA测序、环状DNA测序、eccDNA合成、Circle seq、Circle seq测序。


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