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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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