Fulci Valerio
Dipartimento di Medicina Molecolare. Università di Roma "La Sapienza", Viale Regina Elena, 291 Rome, Italy.
NAR Genom Bioinform. 2025 Apr 17;7(2):lqaf044. doi: 10.1093/nargab/lqaf044. eCollection 2025 Jun.
Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).
最近，有报道称几种将Illumina流动槽或DNA纳米球重新用作空间转录组学RNA捕获装置的方案。这些方案可产生大量测序数据，通常通过使用高性能计算集群进行分析。我报告了空间转录组快速分析（FaST），这是一种基于条形码分析亚细胞分辨率空间转录组学数据集的新型流程。FaST与OpenST、seq-scope、Stereo-seq以及其他可能的方案兼容。它能够在配备32GB内存的标准多核工作站上，在短短1小时内对由超过5亿条读段组成的数据集进行空间分辨转录组的完全重建，包括细胞分割。FaST流程返回适合通过常用软件包（如scanpy或seurat）进行后续分析的RNA分割空间转录组学数据集。值得注意的是，我展示的这个流程依赖于spateo-release软件包进行RNA分割，并且不需要苏木精/伊红或任何其他成像程序来指导细胞分割。不过，与其他用于成像引导细胞分割的软件进行整合仍然是可行的。FaST可在github上公开获取（https://github.com/flcvlr/FaST）。
