NEBnext versus Ion Plus Fragment Library kit

[davehwng]

Hi all,

I'm new to the forum and also new to NGS. Recently, we were donated an Ion PGM with an OT2 set-up. I run a teaching lab (http://bioteach.ubc.ca), and I'm exploring ways to incorporate NGS both into our graduate lab course, our workshops, as well as possible citizen science programming with high school kids.

As a result, our first task is just to set up a decent workflow where we can robustly get data to look at (i.e. our benchmarks are markedly lower as we are not getting "research" relevant data per se and we need to be wary of costs generally). One of our first possible experiments, is to just sequence a small genome using 314 chips (possibly even the e.coli genomic control that is supplied with many of the kits). Here, I see that the Ion Plus kits offered by thermofisher seem to fit the bill, but I also noticed that NEB offers a similar kit but at a greatly reduced cost.

Anyway, I'm wondering why the big difference? And has anyone used the NEBnext kits and found them lacking (and hence I should stick with the more expensive PGMs own line of library prep kits)?

Any help is appreciated!

cheers
dave

[jhalpin]

I have not used the NEBnext kit, but I do regularly use the Kapa BioSciences kit for IonTorrent libraries. It is significantly less expensive than the Life Tech kit and I get much much better results with it. Not including cleanup or barcodes - just the cost for the fragmentation & library kit - I calculate Kapa comes to $29 per sample while Life Tech is $80. Additionally, Kapa provides a much easier workflow.

If you contact Kapa, they will often give you a discount on a "sample" kit to try. See product KK8300 & KK8301. KK8602 is the fragmentation kit, sold separately. I have not purchased their barcodes, as we're swimming in BIOO barcode kits.

https://www.kapabiosystems.com/product-applications/platforms/ion-torrent/library-preparation-for-ion-torrent/

[davehwng]

Thanks for the info. I'm actually trying to see if I can get some sample kits to try for NEB and Thermofisher (and now maybe Kapa as well). NEB has been super accommodating (sending some free stuff - I think they're keen on our plan to see if we can bring some of these procedures to the high school student level), and haven't heard from Thermofisher yet (although they've been great on helping with instrument set up side of things).

[ajthomas]

The Ion Torrent-branded kits are much more expensive and I haven't found them to be any better than others. I've used the NEB kit and it works fine. More recently I tried the Kapa kit and I like it better.

[Lunch_Eater]

@ajthomas
We are looking at comparing NEBNext and Kapa kits for similar reasons. Can you please elaborate on why you like Kapa better than NEB? Thanks.

[ajthomas]

My preference for the Kapa kit is just a personal preference, not that I found it to work better. I didn't do any side-by-side comparison of the two or anything, I just used them both and found that I preferred the Kapa kit.

[jhalpin]

Out of curiosity, does the NEB kit have less cleanup steps?

[valevig]

Hi, only one questio: how many ul of Ion Xpress barcode adaptors (for reaction) do uyo use with the Nebnext kit?
The Nebnext protocol specifies the use of Ion Xpress barcode adaptors for mulitplexed library, but not the volume.

Sorry for the question, but in my lab we have always used the Ion torrent kit, but now we want to try some kits less expensive.
Thanks of all

[seqsuave]

I am looking for cheaper kits for the PGM for around the same purpose, and while I have not done any testing yet, I found some kits that have barcodes included so you done have to worry about Ion Xpress barcodes.

http://www.biooscientific.com/Next-Gen-Sequencing/Ion-PGM-Library-Prep-Kits/NEXTflex-DNA-Seq-Kits