对人类短读序列数据压缩软件的基准研究
Raphael O Betschart1,2, Felix Thalén1, Stefan Blankenberg1,3,4,5
1Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 12, Davos Wolfgang, 7265, Davos, Switzerland.
Scientific reports
|May 2, 2025
概括
有效的数据压缩对于全基因组测序至关重要. 与repaq和SPRING相比,像DRAGEN ORA和Genozip这样的专业工具为fastq.gz文件提供了优越的压缩比.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 数据科学数据科学数据科学
背景情况:
- 全基因组测序产生了大量的数据集,需要有效的数据压缩来存储和传输.
- 对基因组数据的成本效益管理对于大规模的研究计划至关重要.
研究的目的:
- 为了对专用压缩工具对配对的fastq.gz文件的性能进行基准测试.
- 为了将Genozip的BAM文件压缩与SAMtools进行比较.
- 为了评估压缩比,速度和文件格式兼容性.
主要方法:
- 在来自 genome-in-a-bottle 联盟的配对 fastq.gz 文件上对 DRAGEN ORA,Genozip,repaq 和 SPRING 的基因组比较.
- 对Genozip和SAMtools进行BAM文件压缩的比较分析.
- 评估压缩比,压缩/解压缩时间和文件格式支持.
主要成果:
- 所有测试的工具都提供了无损压缩.
- 对于fastq.gz文件,DRAGEN ORA和Genozip实现了大约1:6的压缩比.
- Repaq和SPRING的压缩比较低 (分别为1:2和1:4) 和处理时间更长.
- 对于BAM文件,Genozip比SAMtools提供了比SAMtools更好的约16%的压缩,尽管SAMtools产生了广泛兼容的CRAM文件.
- Genozip支持多种文件格式,与ORA,repaq和SPRING不同,这些文件格式仅限于fastq.gz.
结论:
- 专门的软件有效地压缩配对结尾短读序列数据.
- 商业工具通常提供比自由可用的选项更高的压缩比率.
- 尽管需要许可证,但Genozip提供了高压缩,宽格式支持和可访问源代码的平衡.
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