Long read 16S amplicon Oxford Nanopore data

[Nicholas_Bokulich]

Hi @Shreya ,
It is also possible to classify your reads using kraken2, as @timanix suggests, using the QIIME 2 plugin q2-mosphit. You can find a draft tutorial here:

draft tutorial for shotgun metagenomics with QIIME 2

Hi all, Following on our announcement of the first alpha release of the QIIME 2 Shotgun Metagenomics Distribution, we are starting to develop some alpha (early draft) tutorials. At the moment, we're going to keep these on GitHub and link to specific documents that you can view there. Before too long, we'll be starting to build and host Jupyter Books that cover tutorials for the different QIIME 2 distributions that are available. So, here's a first iteration of a bring-your-own-data tutorial co…

Just don't try to use bracken to normalize the counts, as this method does not appear to be compatible with long-read nanopore data.

Good luck!