文章基本信息

标题：Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ
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作者：Ilia Minkin ; Paul Medvedev
期刊名称：iScience
印刷版ISSN：2589-0042
出版年度：2020
卷号：23
期号：6
页码：1-17
DOI：10.1016/j.isci.2020.101224
语种：English
出版社：Elsevier
摘要：SummaryPairwise whole-genome homology mapping is the problem of finding all pairs of homologous intervals between a pair of genomes. As the number of available whole genomes has been rising dramatically in the last few years, there has been a need for more scalable homology mappers. In this paper, we develop an algorithm (BubbZ) for computing whole-genome pairwise homology mappings, especially in the context of all-to-all comparison for multiple genomes. BubbZ is based on an algorithm for computing chains in compacted de Bruijn graphs. We evaluate BubbZ on simulated datasets, a dataset composed of 16 long mouse genomes, and a large dataset of 1,600 Salmonella genomes. We show up to approximately an order of magnitude speed improvement, compared with MashMap2 and Minimap2, while retaining similar accuracy.Graphical AbstractDisplay OmittedHighlights•BubbZ is a fast whole-genome homology mapper•Works by finding pairwise chains in the compacted de Bruijn graph•Optimized for all-against-all mappings between multiple assembled sequences•Tested on 16 mice and 1,600 Salmonella, offers up to an order of magnitude speed-upAlgorithms; Bioinformatics; Genomics