arXivDaily arXiv每日学术速递 周一至周五更新
arXiv 2007.13673cs.DC
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用于MapReduce-Hadoop基因组学的FASTA/Q数据压缩器:轻松节省空间和时间--版本1

FASTA/Q Data Compressors for MapReduce-Hadoop Genomics:Space and Time Savings Made Easy -- Version 1

Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo

摘要:

动机:基因组数据的存储是生命科学的主要成本,主要通过专门的数据压缩方法有效地解决。出于数据生产丰富的同样原因,大数据技术的使用被视为基因组数据存储和处理的未来,MapReduce-Hadoop是领导者。令人惊讶的是,Hadoop中没有一个专用的FASTA/Q压缩器。事实上,他们在那里的部署并不是立即的。这样的艺术状态是有问题的。结果:我们提供了两个不同方向的主要进展。方法上,我们提出了两种通用的方法,与相应的软件,这使得很容易部署一个专门的FASTA/Q压缩器内MapReduce-Hadoop处理存储在分布式Hadoop文件系统的文件,Hadoop的知识很少。实际上,我们提供的证据表明,在Hadoop中部署这些专用压缩器(到目前为止还没有)可以节省大量成本,即,在大型植物基因组上,HDFS数据块减少30%(一个数据块= 128 MB),I/O时间至少加快1.5倍,网络通信时间与使用Hadoop中可用的通用压缩器相当或减少。最后,我们观察到这些结果也适用于Apache Spark框架,当用于处理存储在Hadoop文件系统上的FASTA/Q文件时。

英文摘要:

Motivation: Storage of genomic data is a major cost for the Life Sciences, effectively addressed mostly via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic. Results: We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy a specialized FASTA/Q compressor within MapReduce-Hadoop for processing files stored on the distributed Hadoop File System, with very little knowledge of Hadoop. Practically, we provide evidence that the deployment of those specialized compressors within Hadoop, not available so far, results in major cost savings, i.e., on large plant genomes, 30% less HDFS data blocks (one block=128MB), speed-up of at least x1.5 in I/O time and comparable or reduced network communication time with respect to the use of generic compressors available in Hadoop. Finally, we observe that these results hold also for the Apache Spark framework, when used to process FASTA/Q files stored on the Hadoop File System.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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