STtools: a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data

MOTIVATION: While there are many software pipelines for analyzing spatial transcriptomics (ST) data, few can process ultra-high-resolution datasets generated by emerging technologies. There is a clear need for new software tools that can handle submicrometer resolution ST data with computational scalability without compromising its resolution. RESULTS: We developed STtools, a software pipeline that provides a versatile framework to handle ST datasets with various resolutions, such as the ones produced by Seq-Scope (<1 μm), Slide-seq (10 μm) and VISIUM (100 μm). It automatically processes raw FASTQ files and runs downstream analyses at several folds higher resolution than existing methods. It also generates various visualizations including transcriptome density, cell type mapping, marker gene highlighting and subcellular architectures. AVAILABILITY AND IMPLEMENTATION: STtools is publically available for download at https://github.com/seqscope/STtools SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.