16s metagenomics kit from Ion Torrent

My group has been using the Ion 16s metagenomics kit from Ion Torrent. This kit has 6 unpublished primers targeting regions: v2, v3, v4, v67, v8 and v9. I have a way to separate the reads out into their targeted regions and am left with a fasta file for each region.

Can qiime 2 be used at the fasta file step and can anyone provide any guidance for this?

Does qiime2 have any guidelines with using Ion Torrent sequencing data?

Many regards,

Hi @Jen_S,

Yes. It sounds like you have demultiplexed sequences but I am not sure of the exact format (you will need to provide more details) but if you can get these into a format similar to qiime1 demultiplexed sequences, you can use the following command to import:

qiime tools import 
–input-path seqs.fna 
–output-path seqs.qza 
–type SampleData[Sequences]

Not yet — we do not have much experience with this format and have only had a few users working with this format (which is to say that we are very interested in learning more to support this format :smile:).

There have been a few other posts about ion torrent data on the forum (e.g., here). If you do run into specific problems with importing, I would recommend first trawling the forum to see what other users have recommended in the past.

I hope that helps!

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