Full-length transcript sequencing of 10X libraries with ONT sequencing

Combining short & long reads at the single cell level.

In addition to Illumina short-read sequencing of a 10x single-cell library, it is possible to get full-length data of transcripts using Oxford Nanopore sequencing (ONT). Long-read sequencing enables detection of e.g. isoform expression, alternative splicing and structural variants.

Please contact us if you want to discuss a short + long-read 10X project!

How it works

NGI performs the standard 10X Genomics library construction according to your kit of choice, producing a tagmented library for short read sequencing. In parallel, an aliquot of cDNA is used to construct a library for ONT sequencing. Both short-read and long read sequence data is delivered.

The short read data are typically used for gene counting and cell cluster generation. The transcript variants from the long read ONT library can then be mapped to specific cell clusters for increased biological insight.

Sample compatibility

cDNA from 3’GE, 5’GE and Multiome kits can be used.  

Last Updated: 26th June 2024

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Relevant Technologies
Method Status


We are currently testing this method. Please contact us to find out more.