Single-cell sequencing is typically done using platforms that generate short reads from the 5' or 3' ends of the transcripts. However, this provides no information on isoform variations in the cells, although it is known that isoforms are highly prevalent in complex eukaryotes. 

In contrast, long-read sequencing (ONT or PacBio) enables the sequencing of full-length transcripts, capturing all isoform variations in the cell. The scywalker tool was designed to analyze long-read single-cell data to generate gene and transcript count matrices that can be further analyzed to compare gene and isoform expression between samples and cell types.