文章基本信息

标题：Detecting Mutations by eBWT
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作者：Nicola Prezza ; Nadia Pisanti ; Marinella Sciortino 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：1-15
DOI：10.4230/LIPIcs.WABI.2018.3
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in the eBWT of the reads collection, and we develop a tool finding SNPs with a simple scan of the eBWT and LCP arrays. Preliminary results show that our method requires much less coverage than state-of-the-art tools while drastically improving precision and sensitivity.
关键词：BWT; LCP Array; SNPs; Reference-free; Assembly-free