Table 1.

Software packages for peak calling

Name	CLIP-seq protocol	Pre- process	Input	Control	Statistical model	Feature	Resolution
Piranha	All	No	BED and BAM	Yes	Zero-truncated negative binomial distribution (default)	Choices of statistical model and covariates	Bins
ASPeak	CLIP-seq and RIP-seq	No	SAM, BAM, BOWTIE and BED	Yes	Negative binomial distribution	Expression sensitive	Peaks
Pyicoclip	All	Yes	Eland, SAM, BAM and BED	No	Background estimation	Complete pipeline	Predefined regions
iCount	iCLIP	Yes	BAM	No	Background estimation	Complete pipeline	Peaks
CLIPper	eCLIP	Yes	BAM	Yes	Poisson distribution	Cubic splines fit of reads profile	Peaks
PARalyzer	PAR-CLIP	Yes	SAM, BAM and BOWTIE	No	Gaussian kernel density estimator	N/A	Reads clusters
Bmix	PAR-CLIP	No	BAM	No	Constrained three-component binomial mixture model	Explicitly accounts for the sources of noise	Reads clusters
WavClusteR	PAR-CLIP	No	BAM	No	Non-parametric, two component mixture model	Complete pipeline	Reads clusters
MiClip	CLIP-seq, HITS-CLIP and PAR-CLIP	No	SAM	No	Zero inflated binomial distribution	Online interface	Reads clusters
pyCRAC	HITS-CLIP, PAR-CLIP and CRAC	Yes	SAM, BAM and Novoalign	No	Background estimation	Complete pipeline	Reads clusters
PureCLIP	eCLIP	No	BAM	Yes	Zero-truncated negative binomial distribution	Integrates motif information	Single nucleotide
PIPECLIP	HITS-CLIP, PAR-CLIP and iCLIP	Yes	BAM	Yes	Zero-truncated negative binomial distribution	Online interface	Reads clusters
CTK	All	Yes	BED	No	Background estimation	Complete pipeline	Single nucleotide