Table 1. Overview of circRNA detection methods.

Tool	De novo?	Check splice site	Realignment	Single-end?	Mapper	Version
acfs	yes	full	yes	yes	BWA-MEM	2.2
segemehl	yes	no	no	yes	segemehl	0.2.0
CIRCexplorer	no	GU-AG GC-AG AU-AC	no	yes	STAR	1.1.3
KNIFE	no	no	no	yes	Bowtie1 and 2	NA
MapSplice2	no	no	no	yes	Bowtie1	2.2.0
circRNA_finder	yes	GU-AG GC-AG AU-AC	no	no	STAR	NA
CIRI	yes	GU-AG	no	yes*	BWA-MEM	1.2
find_circ	yes	GU-AG	no	no	Bowtie2	1.0

^*Although CIRI can take in SE reads, it never finishes within 10000 min in our simulations.