Classification of Illumina MiSeq and Sanger sequences into same OTUs

Hello everyone,

I have sequenced the 18S from individual fungal spores using Sanger sequencing and then I sequenced a community of fungi from the same samples (plant roots) using Illumina MiSeq. I used the same primers for both types of sequencing and I would like to be able to compare directly the fungal communities from spores and from roots.
I followed the MiSeq SOP to classify the Illumina sequences into phylotypes (not OTUs as the dist.seq command produced too large a matrix).
Now I would like to know whether the sequences generated by Sanger belong to the same phylotypes found in the MiSeq dataset.
Is there a way to do that with mothur?

Thanks very much.

You could merge the datasets before align.seqs and take them through the rest of the pipeline. That’s all we have right now. But stay tuned in the next few months we should have something we’re ready to release.


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