biostudies-literatureUnknown41(9)Trull ACivitan International Research Center<h4>Motivation</h4>Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge.<h4>Results</h4>Here, we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and tranBioinformatics (Oxford, England)btaf487https://www.ebi.ac.uk/biostudies/studies/S-EPMC12449243biostudies-literaturescnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.PMC12449243Worthey EAIanov LTrull Afalsescnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.<h4>Motivation</h4>Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge.<h4>Results</h4>Here, we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and tran2025-01-01T00:00:00Z2025 Sep2026-06-03T14:36:30.841Z2026-05-29T03:04:58.847ZS-EPMC124492434090562510.1093/bioinformatics/btaf487