Fig. 3

Snuupy assigns cell barcodes and UMIs for Nanopore reads according to the information from Illumina data. a Flowchart shows the difference between snuupy and Sicelore. b Overlap between snuupy and Sicelore allocated reads. c Numbers of UMIs (left) and genes (right) detected in each nucleus from the Illumina and Nanopore data. d UMAP visualization of the root cell types clustered using abundance information from the Nanopore single-nucleus data. The cell color is the same as in Fig. 1c. e UMAP visualization of the integration of two datasets. The batch effect is removed by Scanorama [30]. Alignment score is calculated by Scanorama and in the range from 0 to 1. Higher alignment score indicates a higher similarity between a pair of datasets