Genotype-free demultiplexing of pooled single-cell RNA-seq

Table 1 Overview of accuracy and performance of scSplit on simulated mixed samples, with one CPU and 30GB RAM

Simulation	sim2	sim3	sim4	sim8	sim12	sim16	sim24	sim32
Mixed samples	2	3	4	8	12	16	24	32
Number of cells	12 383	12 383	12 383	12 383	12 383	12 383	12 383	12 383
Reads per cell	4 973	4 973	4 973	4 973	4 973	4 973	4 973	4 973
Informative SNVs	34 116	34 116	34 116	34 116	34 116	34 116	34 116	34 116
Assigning cells	41 min	41 min	46 min	47 min	1h54m	2h11	2h33	2h55
Singlet TPR	0.97	0.97	0.97	0.97	0.97	0.97	0.96	0.96
Singlet FDR	0	9E −5	9E −5	9E −5	0	0	5E −3	8E −3
Doublet TPR	0.997	0.997	0.997	0.997	0.997	0.997	0.995	0.997
Doublet FDR	0	0	0	0	0	0	0	0
Cohen’s Kappa	1.0	1.0	1.0	1.0	1.0	1.0	0.97	0.98

We used PBMC donor B [2] and genotype data from demuxlet [6] as simulation templates

ISSN: 1474-760X