Abstract Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes.Current methods for transcript identification LADIES SHIRTS CAREER and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference.We present RATTLE, a tool to perform reference-free E-Prom Chip reconstruction and quantification of transcripts using only Nanopore reads.Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.