Table 1.

Summary of computational approaches for detection and quantification of alternative splicing events in single cells.

Computational method	Software/Statistical method	Read aligner	No. of cells	Cell type(s)	Sample origin	Library preparation	Sequencing platform	Isoform variant analysed	Reference
Developed for bulk short-read RNA-sequencing	MISO	Bowtie	12	LNCaP, PC3, T24	Cell line	Smart-Seq	Genome Analyzer IIx, 150 bp PE	CE	[56]
	MISO	Bowtie	18	BMDCs	Mouse	Smart-Seq	HiSeq 2000, 100 bp PE	CE	[14]
	MISO	STAR	34	ESCs	Human	Smart-Seq	HiSeq 2000, 100 bp SE	CE	[73] (Data from [74])
	MISO	Bowtie	18	BMDCs	Mouse	Smart-Seq	HiSeq 2000, 100 bp PE	CE	[78] (Data from [14])
	VAST-TOOLS	TopHat	66	Spermatogenic cells	Mouse	Smart-Seq	HiSeq 4000, 150 bp PE	CE, RI, A5SS, A3SS	[74]
	bam2ssj	Bowtie	10	GM12878	Cell line	Smart-Seq	HiSeq 2000, 100 bp SE	SJ	[72]
	IPSA	TopHat	40	HeLa S3	Cell line	MIRALCS	HiSeq 2000, 150 bp PE, 50 bp SE	SJ	[61]
Developed for single-cell short-read RNA-sequencing	Custom pipeline	ABI whole transcriptome software tool	1	Blastomere	Mouse	Modified single-cell cDNA amplification for microarray	SOLiD sequencer, 50 bp PE	SJ	[54]
	Custom pipeline	ABI whole transcriptome software tool	33	ESCs, ICM, Epiblast, ICM outgrowth cells1	Mouse	Modified single-cell cDNA amplification for microarray	SOLiD sequencer, 50 bp PE	SJ	[53]
	Custom pipeline	Bowtie	85	ESCs, embryonic fibroblast	Mouse	STRT	Genome Analyzer IIx, 150 bp PE	SJ	[55]
	SingleSplice	GSNAP/GMAP	182	ESCs	Mouse	Smart-Seq	HiSeq 2000, 100 bp, PE	Isoform switching	[32] (Data from [70])
	ISOP	Bowtie	384 96 305 96	MDA-MB-231 HTC116 Primary myoblasts Primary glioma	Cell line Cell line Human Human	Smart-Seq Smart-Seq Smart-Seq Smart-Seq	HiSeq 2000, 100 bp PE HiSeq 2000, 150 bp PE HiSeq 2500, 100 bp PE HiSeq 2500, 100 bp PE	Isoform switching	[69] (Additional data from [71], [110], [111]
	Logistic regression	Bowtie STAR STAR	182 1529 31,831	Primary myoblasts ESCs T cells	Human Human Human	Smart-Seq Smart-Seq 10x Genomics	HiSeq 2500, 100 bp PE HiSeq 2000, 100 bp SE NextSeq 500, 75 bp PE	Isoform switching	[68] (Data from [71], [112], [113]
	BRIE	HISAT	40	ESCs	Mouse	Smart-Seq	HiSeq 2500, bp, SE	CE	[31] (Data from [114])
	BRIE	STAR	93 93	iPSCs Endoderm	Human Human	scM&T-seq	HiSeq 2500	CE	[86]
	BRIE	STAR	2208	Oligodendrocytes	Mouse	Smart-Seq	HiSeq X Ten, 50 bp, SE	CE	[29]
	BRIE	STAR	242	Epithelial breast cancer cells	Human	Smart-Seq	HiSeq 2500, 100 bp PE	CE	[84] (Data from [115])
	BRIE	Bowtie	82	Macrophages	Mouse	Smart-Seq	NextSeq 500, PE	CE	[83]
	Expedition	STAR	63 73 70	iPSCs NPCs MNs	Human	Smart-Seq	HiSeq 2000, 100 bp PE	CE, MXE	[43]
Developed for single-cell long-read RNA-sequencing	Custom pipeline	GMAP	2 4	VLMCs Oligodendrocytes	Mouse	STRT	PacBio SMRT	CE, A5SS, A3SS, TSS, TTS	[62]
	Custom pipeline	STARlong	6627	Cerebellar cells	Mouse	Smart-Seq	PacBio SMRT	SJ, CE, TSS, TES	[28]
	Mandalorion	STAR	7	B1a cells	Mouse	Smart-Seq	ONT MinION, 2D	CE, RI, A5SS, A3SS, TSS, TES	[65]
	Mandalorion	STAR	12	OHCs	Mouse	Smart-Seq	ONT MinION, 1D	CE	[67]
	Mandalorion	Minimap2	96	B cells	Human	R2C2	ONT MinION, 1D	CE, RI, TSS, TES	[66]
	IgBLAST, BLASTN	Minimap2	6027	Lymph node cells	Human	Droplet-based (10x Genomics)	ONT MinION, 1D	CE, RI, A5SS, A3SS, TSS, TES	[30]

A3SS: Alternative 3′ splice site; A5SS: Alternative 5′ splice site; ABI: Applied Biosystems; BMDCs: Bone-marrow-derived dendritic cells; CE: Cassette exon; ESCs: Embryonic stem cells; ICM: Inner cell mass; IPSA: Integrative Pipeline for Splicing Analyses; iPSCs: Induced pluripotent stem cells; ISOP: ISOform-Patterns; MIRALCS: Microwell full-length mRNA amplification and library construction system; MISO: Mixture of Isoforms; MN: Motor neurons; MXE: Mutually exclusive exons; NPC: Neural progenitor cells; OHC: Outer hair cells; ONT: Oxford Nanopore Technology; PacBio SMRT: Pacific Biosciences Single Molecule Real Time; PE: Paired-end; R2C2: Rolling Circle Amplification to Concatemeric Consensus; RI: Retained-intron; scM&T-seq: Single-cell methylation and transcriptome sequencing; SE: Single-end; SJ: Splice junction; STRT: Single-cell tagged reverse transcription; TES: Transcription end site; TSS: Transcription start site; VLMCs: Vascular and leptomeningeal cells.

¹Day 3 Oct4⁺Sox2⁺Nanog⁺, day 5 Oct4⁻⁻Sox2⁺Nanog⁺, day 5 Oct4⁻⁻Sox2⁻⁻Nanog⁻⁻ outgrowth cells.