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##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). The pros and cons of each type of kit are listed below:  + 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}.  + 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}.  When growing bacteria in culture as described in this workflow, it should almost always be possible to get enough DNA to use PCR-free TruSeq and therefore minimize library preparation biases in the genome assembly.