School of Information, Yunnan University, Chenggong Campus, Kunming, Yunnan, China.
BMC Bioinformatics. 2022 Jul 23;23(1):294. doi: 10.1186/s12859-022-04837-1.
Over the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, compression of the quality score is a key and difficult aspect of FASTQ file compression. Throughout the literature, we found that the majority of the current quality score compression methods do not support random access. Based on the above consideration, it is reasonable to investigate a lossless quality score compressor with a high compression rate, a fast compression and decompression speed, and support for random access.
In this paper, we propose CMIC, an adaptive and random access supported compressor for lossless compression of quality score sequences. CMIC is an acronym of the four steps (classification, mapping, indexing and compression) in the paper. Its framework consists of the following four parts: classification, mapping, indexing, and compression. The experimental results show that our compressor has good performance in terms of compression rates on all the tested datasets. The file sizes are reduced by up to 21.91% when compared with LCQS. In terms of compression speed, CMIC is better than all other compressors on most of the tested cases. In terms of random access speed, the CMIC is faster than the LCQS, which provides a random access function for compressed quality scores.
CMIC is a compressor that is especially designed for quality score sequences, which has good performance in terms of compression rate, compression speed, decompression speed, and random access speed. The CMIC can be obtained in the following way: https://github.com/Humonex/Cmic .
在过去的几十年中，新技术的出现和成熟极大地降低了基因组测序的成本。因此，需要存储和传输的基因组数据量呈指数级增长。对于标准测序数据格式 FASTQ，质量分数的压缩是 FASTQ 文件压缩的一个关键且困难的方面。在整个文献中，我们发现大多数当前的质量分数压缩方法不支持随机访问。基于上述考虑，研究一种具有高压缩率、快速压缩和解压缩速度以及支持随机访问的无损质量分数压缩器是合理的。
在本文中，我们提出了 CMIC，这是一种用于无损压缩质量分数序列的自适应和支持随机访问的压缩器。CMIC 是本文中四个步骤（分类、映射、索引和压缩）的缩写。它的框架由以下四个部分组成：分类、映射、索引和压缩。实验结果表明，我们的压缩器在所有测试数据集上的压缩率方面都具有良好的性能。与 LCQS 相比，文件大小最多减少了 21.91%。在压缩速度方面，CMIC 在大多数测试案例中都优于所有其他压缩器。在随机访问速度方面，CMIC 比提供压缩质量分数随机访问功能的 LCQS 更快。
CMIC 是一种专门为质量分数序列设计的压缩器，在压缩率、压缩速度、解压缩速度和随机访问速度方面都具有良好的性能。CMIC 可以通过以下方式获得：https://github.com/Humonex/Cmic。
