deletions | additions       diff --git a/Library Preparation and Sequencing .md b/Library Preparation and Sequencing .md  index 17856fb..1dba31a 100644  --- a/Library Preparation and Sequencing .md  +++ b/Library Preparation and Sequencing .md 
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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 provider 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 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 by eliminating PCR, resulting in better assemblies. _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.