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SeQual-Stream: approaching stream processing to quality control of NGS datasets.

Óscar Castellanos-Rodríguez1, Roberto R Expósito2, Juan Touriño2

  • 1Universidade da Coruña, CITIC, Computer Architecture Group, Campus de Elviña, 15071, A Coruña, Spain. oscar.castellanos@udc.es.

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|October 27, 2023
PubMed
Summary

SeQual-Stream offers a novel streaming approach for DNA sequence quality control, significantly improving processing speed and scalability for large genomic datasets. This method accelerates preprocessing during data download and transfer, outperforming traditional batch methods.

Keywords:
Apache SparkBig dataNext generation sequencing (NGS)Quality controlStream processing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Quality control of DNA sequences is crucial for genomic analyses.
  • Existing parallel tools use batch processing, requiring complete datasets upfront.
  • This batch model limits performance when datasets are remotely downloaded or transferred.

Purpose of the Study:

  • Introduce SeQual-Stream, a streaming tool for efficient genomic data quality control.
  • Enable fast, distributed, and scalable quality control operations.
  • Overcome limitations of batch processing for large, dynamically accessed datasets.

Main Methods:

  • Utilizes the Apache Spark framework for distributed stream processing.
  • Leverages Hadoop Distributed File System (HDFS) for data handling.
  • Implements a stream processing paradigm to accelerate preprocessing during data ingestion.

Main Results:

  • SeQual-Stream demonstrates significant improvements in execution times compared to batch tools.
  • Achieved a maximum speedup of 2.7x on datasets exceeding 250 million DNA sequences.
  • Exhibits strong scalability features for handling large-scale genomic data.

Conclusions:

  • SeQual-Stream offers a more scalable and performant solution for genomic data quality control.
  • The tool effectively utilizes stream processing for enhanced efficiency.
  • It is available as free, open-source software under the GNU AGPLv3 license.