Table 2.

circRNA identification tools.

Tools	Language	Prerequisites	Input	PMID
find_circ	Python	Python (2.7) (numpy, pysam) Bowtie2 SAMtools	reads in fastq	23446348
MapSplice2	Python	g++ (≥4.3.3) Python (≥2.4.3) SAMtools Bowtie	reads in fasta/fastq	20802226
Segemehl	C	NA	reads in fasta	1975021224512684
circExplorer2	Python	Python (≥2.7) (pysam ≥ 0.8.4, pybedtools, pandas, docopt, and scipy) TopHat (≥2.0.9) Cufflinks (≥2.1.1) BEDTools genePredToGtf gtfToGenePred bedGraphToBigWig (optional) bedToBigBed (optional) STAR (≥2.4.0j) MapSplice (≥2.1.9) BWA (≥0.6.2-r126) segemehl (≥0.2.0)	reads in fastq	27365365
circRNA_Finder	Perl	Perl awk STAR (versions 2.4.1c) samtools	reads in fasta	25544350
CIRI	Perl	Perl	alignment in SAM	2558336528334140
ACFS	Perl	BWA-0.7.3a Perl BLAT (optional)	reads in fasta	27929140
KNIFE	Perl, Python & R	Bowtie2 (≥2.2.1) Bowtie (≥0.12.7) Perl Python 2.7.5 (numpy, scipy) R 3.0.2 (data.table) SAMtools	reads in fastq	26076956
NCLscan	Python & C++	Python 2.7 BEDTools SAMtools BLAT BWA	reads in fasta	26442529
DCC	Python	Python (pysam, pandas, numpy, and HTSeq)	alignment in BAM	26556385
UROBORUS	Perl	TopHat SAMtools Bowtie1/Bowtie2	alignment in SAM	26873924