Table 1.

Methods of isoform or splicing analysis from RNA-seq. We summarized a collection of benchmark characteristics from simulated studies, literature reviews [142], [143], [144], and software documentation. Abbreviations: ICA: isoform-centric approaches; ECA: exon-centric approaches; EM: expectation maximization algorithm; VB: variational Bayes inference algorithm, MCMC: Markov chain Monte Carlo.

	Methods	Speed	Alignment-free	Novel transcript/splicing event discovery	Major algorithm	Input format	Memory Usage	Multi-threading
Cufflinks	ICA	Relative slow	No	Yes	EM	SAM/BAM	Medium	Yes
StringTie	ICA	Fast	No	Yes	Network flow	SAM/BAM	Medium	No
RSEM	ICA	Relative slow	No	No	EM	SAM/BAM/FASTQ	Medium	No
WemIQ	ICA	Fast	No	No	EM	SAM	Medium	No
eXpress	ICA	Fast	No	No	EM	SAM/BAM	Small	Yes
Sailfish	ICA	Extremely fast	Yes	No	EM, VB	FASTA/FASTQ	Small	Yes
Kallisto	ICA	Very fast	Yes	No	EM	FASTA/FASTQ	Small	Yes
Salmon	ICA	Very fast	Yes	No	EM, VB	SAM/BAM/FASTQ	Small	Yes
MISO	ECA	Fast	No	No	MCMC	SAM	Small	Yes
SUPPA	ECA	Fast	No	Yes (with de novo assembler)	Density-based clustering algorithm	Expression in TPM	Small	Yes
SplAdder	ECA	Fast	No	Yes	Splicing graph	BAM, GTF/GFF	Small	No