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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 dependent 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. The requisite time and ancillary consumables and equipment must also be taken into account (see Figure \ref{fig:cost}). Most sequencing facilities offer library preparation services.  ##Kit Options  Whether you chose to make libraries yourself or use a service provider, the next major choice is of the type of kit. The two most popular 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._ New England Biolabs and Kapa Bioscience). In addition, there have been cost-saving modifications to the Illumina kits (e.g. (for example  \cite{Baym_2015}. The pros and cons of each type of kit are listed below: + TruSeq (our recommendation): _Pro_ – The PCR-free protocol minimizes library bias by using mechanical instead of enzymatic DNA fragmentation, and the elimination of PCR results in better assemblies. _Con_ – requires a large amount of DNA (at least 1 ug for PCR-free). There is also now a TruSeq LT kit which only requires 100ng of DNA and a reduced number of PCR cycles. This may provide a middle option between PCR-free TruSeq and Nextera.  + Nextera: _Pro_ – It allows for 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\cite{Aird_2011}.