TABLE 1.

Summary of trade-offs among five RADseq methods.

	Original RAD	2bRAD	GBS	ddRAD	ezRAD
Options for tailoring number of loci	Change restriction enzyme	Change restriction enzyme	Change restriction enzyme	Change restriction enzyme or size selection window	Change restriction enzyme or size selection window
Number of loci per 1 Mb of genome size*	30–500	50–1000	5–40	0.3–200	10–800
Length of single-end loci	≤1kb if building contigs; otherwise ≤300bp**	33–36bp	<300bp**	≤300bp**	≤300bp**
Cost per barcoded/indexed sample	Low	Low	Low	Low	High
Effort per barcoded/indexed sample	Medium	Low	Low	Low	High
Uses proprietary kit?	No	No	No	No	Yes
Can identify PCR duplicates?	with paired-end sequencing	No	with degenerate barcodes	with degenerate barcodes	No
Specialized equipment needed	Sonicator	None	None	Pippin Prep***	Pippin Prep***
Suitability for large or complex genomes****	good	poor	moderate	good	good
Suitability for de novo locus identification (no reference genome)*****	good	poor	moderate	moderate	moderate
Available from commercial companies (in 2015)	Yes	No	Yes	Yes	No

^*Estimated as follows: original RAD, assuming either a 6-cutter or 8-cutter; 2bRAD, assuming type IIB enzymes with recognition sites containing 5–7 specific nucleotides; GBS, values from Elshire et al.⁶⁶; ddRAD, from Table 1 in Peterson et al¹⁴ and allowing for up to double the size range; ezRAD, values from Toonen et al¹⁶ for species with reference genomes.

^**Based on current limits in sequencing technology

^***Can alternatively be used with standard gel equipment

^****Based on ability to reduce total number of loci and lengths of loci

^*****Based on lengths of loci to distinguish paralogs and duplicate sequence