RE: Attention Ion Torrent 16S Metagenomics Kit Users: Feedback Wanted

Dear Justine,
I hope this message finds you well, I am writing to you from Chile, my name is Roddy Jorquera and I m doing my postdoc at a Non Profit organization health cancer clinic. We are implementing Ion Torrent 16S analysis (i read all the posts in here, loved it: Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2? - #22 by Nicholas_Bokulich)
I would love to try using “sidle” since I m using 16S metagenomics kit and I think using Qiime1 is not my best option (within Ion Reporter, last verion May,2021, they still have qiime1).
Please, could you help me? is the tutorial the guys talk about in those posts, available somewhere? where can I get the IonTorrent primer sequences required for sidle? what do you think about NEPHELE (https://nephele.niaid.nih.gov/) … I have so many questions :frowning: sorry
I would really appreciate any guidance you could provide, I am stuck, using nephele at the momment to test our lab workflow results using the patform…
We are working with human fecal samples and generating latinamerican data for cancer reaserch, I am as stuck as excited about it =)
Thank you in advance,
Best regards.
Roddy

Hi @Roddyjocif,

Thanks for the message and your excitementa bout Sidle! I made it public so other people can benefit from the discussion.

I think pretty much everyone agrees that QIIME 1 is not the best option anymore from a lot of perspectives! Our preprint shows that Sidle out performs OTU clustering, which is what you might get out of QIIME 1. (And that’s ignoring the whole thing where the old version of usearch that’s default there is out of date.)

The sidle tutorial is here. (You can also check out the plugin page which links out to the code and tutorial.) Sidle should work with qiime2-2020.8 and later (altough I think the first official release is 2020.11.) I suggest checking your versions carefully since Sidle relies on RESCRIPt and sometimes there are small upstream shifts that break both libraries.

I’m not sure; you would either need to find them in the documentation or possibly look in the sequences. I haven’t had the opportunity to play with Ion Torrent data much, yet.

I’m unfamiliar with NEPHELE, so I don’t have any ability to comment.

Good luck with your work!

Best,
Justine

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Hi Justine,
Thank you for your replay, I believe Sidle should be part of an analysis pipeline dealing with data from 16S metagenomics kit…The bottleneck I am facing so far is to obtain the primers sequences from Thermofisher, aparently, they would rather make a thermofisher bioinformatician split (variable regions) the fastq files for me, than facilitating the primer sequences.
Nephele is a very useful and friendly plattform, they support standard Ion Torrent data sets altough not focus support for 16S Kit yet.
I ll share my progress with you all in the forum. Hope this can help others dealing with similar issues…

Best,
Roddy

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Hi @Roddyjocif,

I think getting the primer sequences for analysis continues to be a bottle neck. Please let us know how it goes!

I’m not sure how to help.

Best,
Justine