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##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. New England Biolabs and Kappa Bioscience). The pros and cons of each type of kit are listed below:  + Nextera: Pro _Pro_  – It allows for very low amounts of input DNA, down to 1ng in the case of the Nextera XT kit. Con _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 _Pro_  – The PCR-free protocol minimizes library bias by using mechanical instead of enzymatic DNA fragmentation, and by eliminating PCR, resulting in better assemblies. Con _Con_  – requires a large amount of DNA (at least 1\(\mu\)g 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. 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.