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Single-cell long-read RNA sequencing combines the cellular resolution of droplet-based methods with the ability to read full-length transcript molecules, giving you a direct window into gene isoforms—the different versions of a gene a cell can produce—in individual cells. If your goal is reliable novel isoform discovery and allele-specific expression, PacBio’s HiFi reads consistently yield higher per-cell gene detection and experimentally validated novel transcripts (Deng et al., 2025), although at a higher per-cell cost (~$0.69 vs. $0.52 for Oxford Nanopore). Oxford Nanopore provides a more budget-friendly route that still delivers robust cell type classification, but with lower gene and isoform accuracy in current benchmarks. When identical cDNA libraries are sequenced on both platforms, the choice of long-read sequencer may have minimal impact on gene quantification (You et al., 2025), so your experimental priorities should drive the decision. For bioinformatics, the wf‑single‑cell pipeline currently offers the most balanced performance on Nanopore data, while Bambu excels at identifying novel isoforms (Hamraoui et al., 2025). This article distills the latest evidence to help you choose the right approach.

Updated 2026-06-09 · Single-Cell RNA-Seq, Long-Read Sequencing, PacBio +11