Horizon 1 1 17 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES Nature Methods 615-620 2020 fdi:010079057 ENG Nature Methods 1548-7091 ISI:000538122800024 6 10.1038/s41592-020-0820-1 https://www.documentation.ird.fr/hor/fdi:010079057 https://www.documentation.ird.fr/intranet/publi/2020/05/010079057.pdf 17 Horizon (IRD) Souporcell clusters single-cell RNA-seq data using genotype information without the use of a genotype reference. Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for samples containing a mixture of genotypes, whether they are natural or experimentally combined. Multiplexing across donors is a popular experimental design that can avoid batch effects, reduce costs and improve doublet detection. By using variants detected in scRNA-seq reads, it is possible to assign cells to their donor of origin and identify cross-genotype doublets that may have highly similar transcriptional profiles, precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA. Ambient RNA is caused by cell lysis before droplet partitioning and is an important confounder of scRNA-seq analysis. Here we develop souporcell, a method to cluster cells using the genetic variants detected within the scRNA-seq reads. We show that it achieves high accuracy on genotype clustering, doublet detection and ambient RNA estimation, as demonstrated across a range of challenging scenarios. 020 UR224