nf-core

nf-core/scrnaseq

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

353 stars 229 forks 353 watchers Nextflow MIT License
10x-genomics 10xgenomics alevin bustools cellranger kallisto nextflow nf-core pipeline rna-seq single-cell star-solo workflow
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1 Open Issue Need Help Last updated: Sep 13, 2026

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Reduce the number of published files from alevin-fry output 7 days ago
enhancement good first issue
nf-core/scrnaseq
353

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Nextflow
#10x-genomics#10xgenomics#alevin#bustools#cellranger#kallisto#nextflow#nf-core#pipeline#rna-seq#single-cell#star-solo#workflow