单体型感知图索引。
Haplotype-aware graph indexes.
机构信息
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
出版信息
Bioinformatics. 2020 Jan 15;36(2):400-407. doi: 10.1093/bioinformatics/btz575.
MOTIVATION
The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.
RESULTS
We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.
AVAILABILITY AND IMPLEMENTATION
Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
变异图工具包（VG）将遗传变异表示为一个图。虽然图中的每条路径都是一个潜在的单倍型，但大多数路径都是真实单倍型的非生物学、不太可能的重组。
结果
我们通过增加单倍型信息来扩充 VG 模型，以识别哪些路径更有可能在自然界中存在。为此，我们开发了一种可扩展的位置 Burrows-Wheeler 变换的图扩展实现。我们通过构建 1000 基因组计划的 5008 个单倍型的全基因组索引和 108070 个 Trans-Omics 用于精准医学冻结 5 号染色体 17 个单倍型的索引，展示了新实现的可扩展性。我们还开发了一种用于简化 k-mer 索引的变异图的算法，而不会在单倍型中丢失任何 k-mer。
可用性和实现
我们的软件可在 https://github.com/vgteam/vg、https://github.com/jltsiren/gbwt 和 https://github.com/jltsiren/gcsa2 上获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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