Hello,
We will soon do our first sequencing run on our new HiSeq 1000 system. In the past, we analyzed NGS data, but we are yet to prepare a library ourselves. I am currently looking into fragmentation methods, mostly to fragment bacterial DNA for metagenomics studies. We have no Covaris system available, so we are not able to follow the protocol suggested by Illumina. However, some collegues have told me of another fragmentation method they used for hybridization. Basically, DNA to fragment is mixed with small glass beads in a 2 ml tube. The tube is then immersed in a sonicator bath for the appropriate time to obtain the right fragment distribution. I am told this protocol allows to generate a homogenous fragment distribution around 400-500 nt.
I was wondering if this protocol could produce fragments suitable for library preparation (if the illumina end-repair protocol is used afterwards) for illumina thru seq sample prep protocol.
Thank you,
Frédéric Raymond
Centre de recherche en infectiologie
Université Laval, Québec, Canada
We will soon do our first sequencing run on our new HiSeq 1000 system. In the past, we analyzed NGS data, but we are yet to prepare a library ourselves. I am currently looking into fragmentation methods, mostly to fragment bacterial DNA for metagenomics studies. We have no Covaris system available, so we are not able to follow the protocol suggested by Illumina. However, some collegues have told me of another fragmentation method they used for hybridization. Basically, DNA to fragment is mixed with small glass beads in a 2 ml tube. The tube is then immersed in a sonicator bath for the appropriate time to obtain the right fragment distribution. I am told this protocol allows to generate a homogenous fragment distribution around 400-500 nt.
I was wondering if this protocol could produce fragments suitable for library preparation (if the illumina end-repair protocol is used afterwards) for illumina thru seq sample prep protocol.
Thank you,
Frédéric Raymond
Centre de recherche en infectiologie
Université Laval, Québec, Canada
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