Current landscape of approaches to scRNA-seq with nanopore sequencers?
Entering edit mode
11 weeks ago
LauferVA 3.8k

Hi biostars,

Ongoing improvements to multiple aspects of Oxford Nanopore (hereinafter, ONTTF) sequencing have led to substantive increases in single-base calling accuracy. Specifically, many of the most important advances have occurred since 2021 ...

Because this is changing so fast, I worry that even fairly recent, well-performed studies and methodologic proposals relating to the use of ONTTF sequencing for single cell-based transcriptomic studies may already be effectively out of date.

Let's take for, instance, COLOR-seq. Because the error correction was being performed primarily due to single base calling accuracy related considerations that now no longer apply to the same degree, if I had to guess, I might venture a guess that other approaches are gaining traction as certain quality related considerations are no longer an overriding concern...

I know that is not a specific question, so let me try to phrase it in a more directed fashion:

Right now, what ideas the cutting edge for scRNA-seq using Oxford Nanopore? Are there any preprints or published articles that address ONTTF-based single cell transcriptomics written after the quality improvements realized of late (improved variant calling, duplex, etc.)

Thank you for your help and insight!

scRNA-seq nanopore single-cell • 240 views

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