Table 1. Comparing solutions for ChIA-PET data analysis.

	Linker trimming	Fuzzy search	Read alignment	PETs detection	PCR removing	Peak calling	Loop detection	Significant loop calling	Quality control	Allele-specific
CPT	Half-linker		batman	Y	Y	Y	Y	Y
ChiaSig								Y
MICC								Y
Mango	Half-linker		bowtie2	Y	Y	Y	Y	Y
ChIA-PET2	Half-linker, Bridge linker	Y	bwa	Y	Y	Y	Y	Y	Y	Y

The blank means the function is not supported by the tool. CPT and Mango is only capable for half-linker ChIA-PET data. ChiaSig and MICC only perform the significant loop calling step. When searching linkers, CPT and Mango use exact search while ChIA-PET2 can apply fuzzy search. Only ChIA-PET2 offers allele-specific analysis and quality control of ChIA-PET data.