RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing
复制标题
RNACache：使用 MinHashing 将 RNA-Seq 读取快速映射到转录组
DOI：
10.1007/978-3-030-77961-0_31
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
B. Schmidt
中科院分区：
文献类型：
--
作者：
J. Cascitti;S. Niebler;A. Müller;B. Schmidt
阅读物与转录组的比对是各种生物信息学RNA-seq管道中重要的初始步骤。由于传统的基于对齐的工具运行时间过长，替代的、无对齐的方法最近变得越来越重要。我们提出了一种新的方法来检测转录本和RNA-seq阅读之间的局部相似性，该方法基于上下文感知的挖掘。我们引入了RNACache，这是一个三步处理流水线，包括对OFK-MERS进行散列处理，基于匹配的(在线)过滤，以及基于覆盖的过滤，以识别真正表达的转录异构体。我们的性能评估显示，RNACache生成高精度的转录映射，与最先进的工具RapMap、Salmon和Kalisto相比，错误匹配显著减少。此外，它还可在普通多核工作站上以低内存消耗提供可扩展且极具竞争力的运行时性能。RNACache可在以下网址公开获得：https://github.com/jcasc/rnacache.
The alignment of reads to a transcriptome is an important initial step in a variety of bioinformatics RNA-seq pipelines. As traditional alignment-based tools suffer from high runtimes, alternative, alignment-free methods have recently gained increasing importance. We present a novel approach to the detection of local similarities between transcriptomes and RNA-seq reads based on context-aware minhashing. We introduce RNACache, a three-step processing pipeline consisting of minhashing ofk-mers, match-based (online) filtering, and coverage-based filtering in order to identify truly expressed transcript isoforms. Our performance evaluation shows that RNACache produces transcriptomic mappings of high accuracy that include significantly fewer erroneous matches compared to the state-of-the-art tools RapMap, Salmon, and Kallisto. Furthermore, it offers scalable and highly competitive runtime performance at low memory consumption on common multi-core workstations. RNACache is publicly available at: https://github.com/jcasc/rnacache.
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
9.8
作者：
Stephens ZD;Lee SY;Faghri F;Campbell RH;Zhai C;Efron MJ;Iyer R;Schatz MC;Sinha S;Robinson GE
通讯作者：
Robinson GE