UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Google Inc., Mountain View, CA, USA.
Science. 2021 Dec 17;374(6574):abg8871. doi: 10.1126/science.abg8871.
We introduce Giraffe, a pangenome short-read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe maps sequencing reads to thousands of human genomes at a speed comparable to that of standard methods mapping to a single reference genome. The increased mapping accuracy enables downstream improvements in genome-wide genotyping pipelines for both small variants and larger structural variants. We used Giraffe to genotype 167,000 structural variants, discovered in long-read studies, in 5202 diverse human genomes that were sequenced using short reads. We conclude that pangenomics facilitates a more comprehensive characterization of variation and, as a result, has the potential to improve many genomic analyses.
我们介绍 Giraffe，这是一种泛基因组短读映射器，能够有效地映射到通过序列图串联的一组单倍型。Giraffe 可以以与标准方法映射到单个参考基因组相当的速度将测序读取映射到数千个人类基因组。提高的映射准确性可以在全基因组基因分型管道中提高小变体和更大结构变体的准确性。我们使用 Giraffe 在使用短读测序的 5202 个多样化人类基因组中对 167000 个长读研究中发现的结构变体进行基因分型。我们的结论是，泛基因组学促进了对变异的更全面描述，因此有可能改善许多基因组分析。
