Longcell a pipeline designed to analyze isoforms from Oxford Nanopore sequencing, enables scRNA-seq Innovation

In the study “Single cell and spatial alternative splicing analysis with Nanopore long read sequencing”, published in Nature Communications, developed Longcell, a novel statistical and computational pipeline designed to analyze isoforms from Oxford Nanopore long reads in single-cell and spatial transcriptomics experiments. Tested on simulated and real-world datasets, Longcell improves isoform quantification and allows reliable detection of isoform switching across cell populations and spatial contexts.

During the work, they examined in detail the main sources of noise in single-cell isoform analysis, showing how UMI dispersion can affect quantification and how exon misalignment or read truncation may lead to false detections of alternative splicing, particularly when reference annotations are missing.

Overview of Longcell

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