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What kit/protocols do you guys use for shotgun metagenomics? We've been using Nextera XT but it's so expensive and looking for a cheaper alternative as we scale up. Are Truseq kits cheaper per sample? Based on list price it doesn't seem that much cheaper, and the hands-on time is certainly higher.
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I've been using half-volumes of Nextera XT reagents to make libraries from metagenomic DNA for shotgun assembly which, well, halves the price (not to state the obvious). Our collaborators go down to even further volumes without a decrease in quality for small genome assembly but I haven't yet validated this on our more complex communities. Are you limited in your input mass at all? If not, you might be interested in this benchmarking paper; if so, take a look at this one.
For reference, I chose the Nextera XT system given the limited mass of my samples and their variety of size distributions, as described here.
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