IMOS: improved Meta-aligner and Minimap2 On Spark

BMC Bioinformatics

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[1] 0000 0001 0740 9747, grid.412553.4, Department of Computer Engineering, Sharif University of Technology, Azadi, Tehran, Iran;

关键词: Aligner;    Long read;    Big data;    Distributed processing;    PacBio;   

DOI  :  10.1186/s12859-018-2592-5

来源: publisher

【 摘 要 】

BackgroundLong reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed.ResultsIn this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM) enhancing both its accuracy and speed. IM is up to 6x faster than the original Meta-aligner. It is also implemented to run IM and Minimap2 on Apache Spark for deploying on a cluster of nodes. Moreover, multi-node IMOS is faster than SparkBWA while executing both IM (1.5x) and Minimap2 (25x).ConclusionIn this paper, we purposed an architecture for mapping long reads to a reference. Due to its implementation, IMOS speed can increase almost linearly with respect to the number of nodes in a cluster. Also, it is a multi-platform application able to operate on Linux, Windows, and macOS.

【 授权许可】

CC BY