Table 5.

Advantages/disadvantages of each approaches

Method	Term definition	Advantage	Disadvantage
GBS	Introduced byDavey et al. (2011) Genotyping‐by‐sequencing (GBS) is a set of genetic screening techniques using restriction enzymes to reduce genome complexity and enable high‐throughput genotyping of multiple DNA samples at large number of DNA marker (usually SNPs)	Keep individual information No reference genome required Allow low coverage sequencing Library normalization	High genotyping costs with large number of samplesa Heavy bioinformatics process when dealing with thousands of samples Limited multiplexing for sequencingb
Rapture	Developed byAli et al. (2016) “A sequencing technique, which combine the benefits of both RAD‐seq and sequence capture adding an in‐solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture is a rapid and flexible technology capable of analyzing a very large number of samples with minimal sequencing and library preparation costs.”	Costs decrease with number of samples compared to GBS Keep individual information No reference genome required Allow low coverage sequencing Fast bioinformatic processes Requires fewer reads per sample than GBS for the same coverage	Require prior RAD‐seq experiment to develop capture probes Investment for probes production Overall time required for getting results extended Less cost‐effective when number of samples is small
Pool‐seq	Reviewed bySchlötterer et al. (2014) “A sequencing technique in which sequencing libraries are not prepared from DNA of a single individual or cell but from a mixture of DNA fragments originating from different individuals or cells.”	Low costs Fast library time preparation Large library multiplexing (hundreds to thousands of samples) Fast bioinformatics processes	No individual information Requires genomic reference Require pool of individuals > 40 Unbalanced contribution of samples Minimal coverage > 20×

^aGenotyping costs are proportional to the number of samples.

^bFor the same sequencing depth, GBS need more sequencing effort per sample than Rapture.