Table 1.

Main characteristics of ff estimation tools selected for benchmark in the present study.

ff tools	Main principle	Male specific	Read counting method	GC correction	Input	Output	Programmation language	Repository link
Defrag a	Based on normalized fraction of reads on chromosome Y	Yes	bin (1Mo)	Yes	.bam, .pickle	.csv	Python	https://github.com/VUmcCGP/wisecondor/tree/legacy
Defrag b	Based on fraction of reads uniquely mapped to chromosome Y (subset of chromosome Y)	Yes	bin (1Mo)	Yes	.bam, .pickle	.csv	Python	https://github.com/VUmcCGP/wisecondor/tree/legacy
Seqff	Based on pretrained bin counts	No	bin (50ko)	Yes	.sam	.csv	R	https://obgyn.onlinelibrary.wiley.com/doi/abs/10.1002/pd.4615
iSanefa lcon	Based on the spatial distribution of reads on the estimated nucleosome profiles	No	Read start position	No	.bam	.csv	Python