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RESEARCH PRODUCT

A Big Data Approach for Sequences Indexing on the Cloud via Burrows Wheeler Transform

Mario RandazzoSimona E. Rombo

subject

FOS: Computer and information sciencesArtificial Intelligence (cs.AI)Computer Science - Distributed Parallel and Cluster ComputingComputer Science - Artificial IntelligenceComputer Science - Data Structures and AlgorithmsData_FILESData Structures and Algorithms (cs.DS)Distributed Parallel and Cluster Computing (cs.DC)

description

Indexing sequence data is important in the context of Precision Medicine, where large amounts of ``omics'' data have to be daily collected and analyzed in order to categorize patients and identify the most effective therapies. Here we propose an algorithm for the computation of Burrows Wheeler transform relying on Big Data technologies, i.e., Apache Spark and Hadoop. Our approach is the first that distributes the index computation and not only the input dataset, allowing to fully benefit of the available cloud resources.

yearjournalcountryeditionlanguage
2020-07-20
https://dx.doi.org/10.48550/arxiv.2007.10095