Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE

Table 1 Summary statistics for long-read single-cell datasets

Dataset ID	Sequencing platform	Sequencing kit	Total reads	Pass reads	Mean reads per cell^a	Median accuracy of pass reads (%)	Useable^b reads with Cell Ranger	Useable reads with BLAZE	Useable reads with Sockeye
PromethION	PromethION	SQK-LSK110	100,941,015	61,967,455	60,634	95.1	43,473,150 (70%)	43,001,188 (69%)	43,063,370 (69%)
GridION	GridION	SQK-LSK110	10,371,632	7,521,667	7360	96.0	5,461,630 (73%)	5,430,433 (72%)	5,462,816 (73%)
Q20	GridION	SQK-Q20EA	4,479,225	3,423,062	3349	97.9	2,501,260 (73%)	2,484,366 (73%)	2,511,016 (73%)
scmixology2 (Tian et al. [15])	PromethION	SQK-LSK109	36,927,546	25,164,948	101,471	95.7	18,347,232 (73%)	18,099,553 (72%)	17,818,239 (71%)

^aPass reads divided by the number of Cell Ranger barcodes
^bPass reads that have a valid 10x barcode and a UMI and can be assigned to a barcode in the whitelist

ISSN: 1474-760X