Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison

BMC Genomics

Table 1 Characteristics of the pipelines

Pipeline	Compressed input	Linker chemistry	Bc sets	Adjustable alignment	Ranhex conversion	Algorithm	Programming language
alevin-fry splitp [24, 30,31,32]	Yes	v1,v2	Input	Yes	Yes	Position based	Rust
LR-splitpipe [25, 28]	No	v2	Fixed	Yes	No	Linker based position	Python
SCSit [26, 33]	No	v1	Fixed	Yes	No	Linker based position	C
splitseq-demultiplex [27]	No	Any	Input	Yes	Yes	Alignment/Position based	Python,shell
splitpipe [34]	Yes	v1,v2	Fixed	No	Yes	Position based	Python,shell
splitpipeline [16, 24]	Yes	v1,v2	Input	No	Yes	Position based	Python,shell
STARsolo [22, 29, 35]	Both	Any	Input	Yes	No	Position based	C,C + +
zUMI [23, 36]	Yes	Any	Input	Yes	Yes	Position based	Perl,R,shell,Python

ISSN: 1471-2164