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The first choice in library preparation is whether to do the library prep yourself, or to have the library made by your sequencing provider. The economics of this decision are usually dependant on the number of samples involved. For example an Illumina TruSeq library prep kit costs around $2600 for 48 samples. That's far cheaper than the $150 to $300 that a typical sequencing provider would charge per sample. However, if you're only preparing a couple of samples there's no reason to buy an entire kit. Most sequencing facilities offer library preparation services.  ##Kit Options  Whether you chose to make libraries yourself, or use a provider the next major choice is of the type of kit. The two major different choices with Illumina kits are the Nextera transposase-based kits or the TruSeq kits (with or without PCR). These kits are available from Illumina, but there are also comparable options from other vendors (e.g. ??? and ???). New England Biolabs).  The pros and cons of each type of kit are listed below: + Nextera: Pro – Can use very low amounts of input DNA, down to 1ng in the case of the Nextera XT kit. Con – the transposase has an insertion bias and the extensive PCR required for low input samples will also impact the final assembly.  + TruSeq (our recommendation): Pro – If the PCR-free protocol is used this minimizes bias due to fragmentation (via mechanical shearing) and PCR, resulting in better assemblies. Con – requires a large amount of DNA (1µg for PCR-free). There is also now a TruSeq LT kit which only requires 100ng of DNA but does entail some PCR so may provide a middle option between PCR-free TruSeq and Nextera.