Table 3.

Comparison between ARPEGGIO and other available, non-commercial and general workflows able to work with raw WGBS data. There were a total of 12 workflows found and different features were selected for this comparison. The language indicates the main language(s) used to program the workflow. Polyploid support refers to support analysis of data from a polyploid with no official genome assembly available. Diploid support refers to analysis of data from a diploid or a polyploid with an available official genome assembly. Quality check, alignment, statistical and downstream analyses are all different steps in the data analysis process with downstream analyses being defined as follow-up analyses on DMRs found by the statistical analyses. Methylation contexts are 3 in total: CpG, CHG and CHH and this feature is sometimes limited to CpG only. Visualization represents any script or function allowing the user to visualize the DMRs found by the statistical analyses. Reproducibility is difficult to quantify and in this table a tool was considered reproducible if the corresponding paper mentioned reproducibility as one of their goals

	ARPEGGIO	QUMA	MOABS	QuasR	MethPipe	bicycle	RUbioSeq	WBSA	P3BSseq	Methy-Pipe	MethFlow	snakePipes
Language	Python, R	HTML, Perl, Javascript	C++, Perl	R	C++	Java	Perl	Perl, R	Python	Perl, R	Python, Perl, Java	Python, R
Polyploid support	✓	X	X	X	X	X	X	X	X	X	X	X
Diploid support	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓
Quality check	✓	✓	✓	✓	✓	X	✓	✓	✓	X	X	✓
Alignment	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓	✓
Statistical analyses	✓	✓	✓	✓	✓	✓	X	✓	✓	✓	✓	✓
Methylation context	All	CpG only	All	All	All	All	All	All	All	All	?	CpG only
Downstream analyses	✓	X	X	✓	✓	X	X	✓	X	✓	✓	X
Visualization	X	X	X	✓	✓	X	X	✓	X	✓	✓	X
Reproducibility	✓	–	–	✓	–	✓	–	–	–	–	✓	✓
Paper	–	[72]	[67]	[73]	[74]	[75]	[76]	[77]	[78]	[79]	[80]	[81]