Tweet
Anyone have experience/thoughts on the iGenomX Riptide system? Worth checking out..?
-
-
We have not tried it, but it looks promising for for very large projects - meaning hundreds of samples? -
We just did a Zoom call with them, and I was very impressed. We will order one of their kits when we get in a large number of bacterial DNAs. They are working on RNA kits, but don't offer them yet. They plan to have a ribodepletion kit too, that is very interesting, but I don't think I can describe it in a public forum yet.
The kits have a one year shelf life too (which is great), but you pretty much have to use them in batches of 96.
Although even if you only use 48 samples and toss the rest of that plate, the cost would be in the $20 range per sample... not bad if it works.Comment
-
Pros: high throughput, low cost, simple workflow, quality base calls and mapping rates, tunable for GC, customizable (can add targeted primers), inputs from 1-200+ ng and can accommodate dsDNA or ssDNA inputs (first strand cDNA, WGA, bisulfite converted).
Cons: Current version does not use UDIs (it is dual index, just not unique dual), uses priming + amplification so produces some peaks and valleys in coverage, current format has marginally lower complexity per sample library (so not recommended for low frequency somatic variant detection). Read count correlates with input.
best practices: works best for 96 (or more) samples of same species, same template source.
Common applications: microbial WGS, meta genomic/ microbiome screening, PCR amplicons, and skim-seq / GBS.Comment
-
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.Today, 11:43 AM
-
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... -
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
Comment