Has anyone managed to make mate pair libraries with an insert size of over 5kb as supported by Illumina? Is there anything different in the circularization stage?
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Illumina doesn't support anything but the 2-5kb protocol, currently. But one can ask nicely and they will provide a beta - it doubles the starting material and the volumes(and components) for the first end-repair and biotinylation. I have prep'd a 5kb using both ways and had a better yield to go onto the HiSeq using the 5-10kb beta protocol. Another tip is to start with quality template (dna in my case). -
I have heard that the Broad Institute is using 40kb fragments somehow to produce vertebrate genomes from Illumina, but I don't know any details.Comment
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The Broad strategy first creates 40kb-insert fosmids by traditional cloning, which are then used to generate mate-pair libraries. Details are in the supplement of their recent ALLPATHS-LG paper (Gnerre et al, 2011 PNAS).Comment
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