We performed de novo transcriptome assembly using isONform, RATTLE, RNA-Bloom2, rnaSPAdes, RNA-Bloom2-hybrid, and Trinity on 5 different datasets. Bambu was also used to generate reference-guided assembled transcriptome. (1) Simulated Nanopore PCR-cDNA data and match Illumina short read RNAseq, (2) Nanopore PCR-cDNA sequencing of two human lung cancer cell lines with sequin spike-in transcripts and matched Illumina short read RNAseq, (3) Nanopore direct RNA sequencing of breast and lung cancer cell lines and matched Illumina short read RNAseq, (4) Nanopre PCR-cDNA sequencing of 4 pea cultivars and matched Illumina short read RNAseq, (5) PacBio Kinnex single-cell RNAseq of PBMC data.