Originally posted by luc
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One thing I wanted to point out is that in the post you linked it says "The flaw in our analysis (of course) is that we should have used the Illumina Nextera XT kit for these samples as these are optimized for smaller genomes to minimise excessive numbers of smaller fragments". I believe, as I already said elsewhere in Seqanswer, that the enzyme is exactly the same for the standard and the XT kits (as I joke I always say that Illumina just bought Epicentre, repacked their enzyme and started selling for a few thousand USD but they didn´t make any effort to improve/change it) . What is different is just the buffer, as we also showed in our paper. Therefore, you need a two-buffer system to work with inputs that span from sub-pg to tens of ng DNA. Besides, varying the amount of PEG and the amount of enzyme will enable a better control of the size of the fragments (thus avoiding over-fragmentation). If you believe in coincidences (I don´t) the "long-fragments" and "short fragments" buffers that were used in the old Epicentre kit are the same used now in the Nextera and Nextera XT, respectively.
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