ecDNA is small and heavily rearranged, and existing methods are not sufficient to characterize it. We have therefore developed our own: scEC&T-seq, an experimental and computational technique that profiles the transcriptome and ecDNA sequence of single cells (Chamorro González et al., Nat. Genetics, 2023), and Decoil, a purely computational technique that reconstructs ecDNA structure from long-read sequencing (Giurgiu et al., Genome Research, 2024). Inspired by our micronucleation work, we are currently developing a method to profile ecDNA in single micronuclei.