AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.

IF 3.6 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-08-19 DOI:10.1109/TCBB.2024.3433378

Jeremie S Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu

引用次数: 0

Abstract

AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4×. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants.

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AirLift：快速、全面的参考基因组间重配技术。

AirLift 是第一款读数重映射工具，用户可以将以前映射到一个参考基因组的读数集快速、全面地映射到另一个类似的参考基因组。然后，用户可以针对每个最新发布的参考文献快速运行读数集下游分析。与最先进的读数重映射方法（即完全映射）相比，AirLift 将两个参考基因组版本之间的读数集重映射的总体执行时间缩短了 27.4 倍。我们用 GATK 验证了我们的重映射结果，发现 AirLift 在识别地面实况 SNP/INDEL 变异方面具有很高的准确性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

IEEE/ACM Transactions on Computational Biology and Bioinformatics 工程技术-计算机：跨学科应用

CiteScore

7.50

自引率

6.70%

发文量

479

审稿时长

3 months

期刊介绍： IEEE/ACM Transactions on Computational Biology and Bioinformatics emphasizes the algorithmic, mathematical, statistical and computational methods that are central in bioinformatics and computational biology; the development and testing of effective computer programs in bioinformatics; the development of biological databases; and important biological results that are obtained from the use of these methods, programs and databases; the emerging field of Systems Biology, where many forms of data are used to create a computer-based model of a complex biological system