Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
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DOI：
10.1093/bioinformatics/btaa1017
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发表时间：
2020-12-01
期刊：
影响因子：
5.8
通讯作者：
Weissman, Tsachy
中科院分区：
文献类型：
--
作者：
Chandak, Shubham;Tatwawadi, Kedar;Weissman, Tsachy
动机：纳米孔测序为基因组测序提供了实时和便携式解决方案，与第二代技术相比，能够实现更好的组装、结构变体发现和修饰碱基检测。测序过程以fast 5文件中包含的原始信号的形式生成大量数据，这些数据必须进行压缩以实现有效的存储和传输。由于原始数据是固有的噪声，有损压缩有可能显着降低空间要求，而不会对下游application.Results的性能产生不利影响：我们探索使用两个国家的最先进的有损时间序列压缩器的纳米孔原始数据的有损压缩，并评估压缩大小和basecalling/共识精度之间的权衡。我们在不同覆盖深度的各种数据集上测试了几种碱基判定器和共识工具，并得出结论，与最先进的无损压缩器相比，有损压缩可以使原始数据的压缩大小进一步减少35-50%，对碱基判定准确性（减少小于或接近0.2%）和共识准确性（减少小于或接近0.002%）的影响可以忽略不计。此外，我们评估了有损压缩对甲基化调用准确性的影响，并观察到这种影响对于压缩大小的类似减少是最小的，尽管需要使用改进的基准数据集进行进一步评估才能得出明确的结论。结果表明，有可能在纳米孔测序设备本身上使用有损压缩，以显着降低存储和传输成本，同时保持下游应用的准确性。
Motivation: Nanopore sequencing provides a real-time and portable solution to genomic sequencing, enabling better assembly, structural variant discovery and modified base detection than second generation technologies. The sequencing process generates a huge amount of data in the form of raw signal contained in fast5 files, which must be compressed to enable efficient storage and transfer. Since the raw data is inherently noisy, lossy compression has potential to significantly reduce space requirements without adversely impacting performance of downstream applications.Results: We explore the use of lossy compression for nanopore raw data using two state-of-the-art lossy time-series compressors, and evaluate the tradeoff between compressed size and basecalling/consensus accuracy. We test several basecallers and consensus tools on a variety of datasets at varying depths of coverage, and conclude that lossy compression can provide 35-50% further reduction in compressed size of raw data over the state-of-the-art lossless compressor with negligible impact on basecalling accuracy (less than or similar to 0.2% reduction) and consensus accuracy (less than or similar to 0.002% reduction). In addition, we evaluate the impact of lossy compression on methylation calling accuracy and observe that this impact is minimal for similar reductions in compressed size, although further evaluation with improved benchmark datasets is required for reaching a definite conclusion. The results suggest the possibility of using lossy compression, potentially on the nanopore sequencing device itself, to achieve significant reductions in storage and transmission costs while preserving the accuracy of downstream applications.