Establishing Seq-Scope data processing as a spatial transcriptomics nf-core pipeline

Seq-Scope is a spatial transcriptomic method that generates spatially barcoded spots directly on the Illumina flow cell with high resolution. This means that, in addition to bringing down cost, the spatial resolution of Seq-Scope is determined by the distance between the clusters on the flow cell. Depending on the used flow cell, the spatial resolution can range from 0.5-3 µm and the analyzed area can be up to 1.5 cm2. We expect that this emerging method will find wide adaptation in the spatial omics community. Utilizing the nf-core framework, we are implementing existing tools for processing Seq-Scope data into a reproducible and transparent pipeline. Establishing a Seq-Scope data processing pipeline will additionally pave the way for integration of similar technologies such as Stereo-seq and Pixel-seq, and contribute to the effort of bringing spatial omics to nf-core.