Table 2.

Normalization pipelines for Hi-C data

Software	Authors	Reference originally applied	Software source
Hiclib	Mirny Lab	Lieberman-Aiden, 2009	http://mirnylab.bitbucket.org/hiclib/
Hicpipe	Tanay Lab	Lieberman-Aiden, 2009	http://compgenomics.weizmann.ac.il/tanay/?page_id=283
scell_hicpipe	Tanay Lab	Nagano, 2013	http://compgenomics.weizmann.ac.il/tanay/?page_id=580
Juicebox	Lieberman-Aiden Lab	Rao, 2014	http://www.aidenlab.org/juicebox/

Yaffe and Tanay generated a normalization pipeline that corrects for fragment length, GC content and mappability, following a maximum likelihood optimization procedure. This method has been applied to several Hi-C studies [100, 135]; however, it does rely on prior knowledge about the abovementioned sources of bias. Imakaev et al. developed a computationally less expensive iterative correction procedure, which has also been applied to Hi-C studies [85]. Nagano et al. have introduced a special pipeline for their single-cell protocol [110].