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LW-FQZip 2: a parallelized reference-based compression of FASTQ files.

Zhi-An Huang1, Zhenkun Wen1, Qingjin Deng1

  • 1College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, China.

BMC Bioinformatics
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Summary

A new lossless compression method, LW-FQZip 2, effectively reduces the storage needs for high-throughput DNA sequencing data. This method achieves promising compression ratios with reasonable computational costs, aiding downstream analyses.

Keywords:
High-throughput sequencingReference- based compressionSequence alignmentSequencing data compression

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput DNA sequencing generates massive datasets, creating storage challenges.
  • Decreasing storage costs lag behind data volume growth, necessitating efficient data management solutions.
  • Data compression is crucial for mitigating storage bottlenecks in genomic analyses.

Purpose of the Study:

  • To develop and evaluate a novel lossless compression method for high-throughput DNA sequencing data.
  • To address the storage limitations posed by the increasing volume of sequencing data.
  • To provide an efficient tool for managing large genomic datasets.

Main Methods:

  • Implementation of a lossless reference-based compression algorithm, LW-FQZip 2.
  • Inclusion of a light-weight mapping model, bitwise prediction by partial matching, and arithmetic coding.
  • Utilization of multi-threading parallelism for enhanced performance.

Main Results:

  • LW-FQZip 2 demonstrates promising compression ratios on both short-read and long-read sequencing data.
  • The method achieves these compression ratios within reasonable time and memory usage.
  • LW-FQZip 2 offers an improvement over previous compression techniques through enhanced coding and parallelism.

Conclusions:

  • LW-FQZip 2 is a viable tool for archival and space-constrained applications in high-throughput DNA sequencing.
  • The method effectively addresses the storage bottleneck in genomic data analysis.
  • LW-FQZip 2 is publicly available for research and application.