| 摘要: |
| 细胞之间的关系以及它们在组织样本中的相对位置对理解疾病病理学至关重要，空间转录组(Spatial Transcriptomics,ST)技术作为近年来发展起来的一种新兴技术，为肿瘤细胞的异质性和空间分布研究提供了新的思路。本研究基于空间转录组技术Stereo-seq所取得的测序数据，改进了一种针对生物序列数据的处理框架，并通过优化读写速度、分治优化哈希容器等方式优化空间转录组定位算法。实验结果表明，该定位算法经过优化后耗时由403 s下降至173 s，速度提升1.33倍。 |
| 关键词: 空间转录组 Stereo-seq 哈希映射 生物信息处理 |
| DOI：10.13656/j.cnki.gxkx.20241127.007 |
| 投稿时间：2023-12-17修订日期：2024-01-18 |
| 基金项目:国家重点研发计划课题(2022YFC3400400)资助。 |
|
| Spatial Transcriptome Mapping Algorithm and Speed Optimization |
|
TANG Jianheng, ZHANG Zi
|
| (School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China) |
| Abstract: |
| The interaction between cells and their relative positions in tissue samples are crucial for understanding the pathology of diseases.Spatial transcriptomics (ST),as a technology emerged in recent years,provides new ideas for studying the heterogeneity and spatial distribution of tumor cells.Based on the spatial transcriptome sequencing data obtained by Stereo-seq,a data processing framework for biological sequence data is improved,and the spatial transcriptome mapping algorithm is optimized by optimizing the read/write speed and partitioning the optimized Hash containers.The experimental results show that the elapsed time of the mapping algorithm is reduced from 403 s to 173 s after optimization,which indicates that the speed is increased by 1.33 times. |
| Key words: spatial transcriptomics Stereo-seq Hashmap biological information processing |
