文章基本信息

标题：Haplotype-aware graph indexes
本地全文：下载
作者：Jouni Sir{\'e}n ; Erik Garrison ; Adam M. Novak 等
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2018
卷号：113
页码：1-13
DOI：10.4230/LIPIcs.WABI.2018.4
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. 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 indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.
关键词：FM-indexes; variation graphs; haplotypes