Finding Maximal Exact Matches Using the r-Index.
Finding Maximal Exact Matches Using the r-Index.
复制标题
使用 r 索引查找最大精确匹配。
DOI：
10.1089/cmb.2021.0445
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Boucher,Christina
中科院分区：
文献类型：
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作者：
Rossi,Massimiliano;Oliva,Marco;Bonizzoni,Paola;Langmead,Ben;Gagie,Travis;Boucher,Christina
有效地找到序列读取与基因组数据库之间的最大精确匹配（MEMs）是读取比对的关键一步。但直到最近，人们还不知道如何在空间中构建一个支持高效MEM查找的数据结构，即Burrows-Wheeler变换的运行次数。2021年，Rossi等人展示了如何在空间索引之外构建一个名为thresholds的小型辅助数据结构。这个附加功能可以使用ther-index高效地查找MEM。在本文中，我们将介绍实现此解决方案的工具，我们称之为MONI。也就是说，我们给出了数据结构的主要组成部分的高级视图，并展示了如何下载，编译源代码，并用于在一组序列读取和一组基因组之间查找MEMs。
Efficiently finding maximal exact matches (MEMs) between a sequence read and a database of genomes is a key first step in read alignment. But until recently, it was unknown how to build a data structure in space that supports efficient MEM finding, whereris the number of runs in the Burrows–Wheeler Transform. In 2021, Rossi et al. showed how to build a small auxiliary data structure calledthresholdsin addition to ther-index in space. This addition enables efficient MEM finding using ther-index. In this article, we present the tool that implements this solution, which we call MONI. Namely, we give a high-level view of the main components of the data structure and show how the source code can be downloaded, compiled, and used to find MEMs between a set of sequence reads and a set of genomes.