Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.

Abstract

Recently, several protocols repurposing the Illumina flow cells 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 HPC clusters. I report inhere a novel pipeline for the analysis of high resolution spatial transcriptomics datasets obtained on Illumina flow cells. FaST is compatible with OpenST, seq-scope and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of more than 500 M million reads in as little as two hours on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented ST 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.