Qiime2 18S workflow

[colinbrislawn (Colin J Brislawn)]

Hello Michelle,

Great question! Welcome to the Qiime 2 forums! :qiime2:

The good news is that SILVA includes both 16S and 18S reads. This means that you can download the silva database as shown here, and train an 18S classifier as shown here.

Other than changing the taxonomy assignment step, the process is the same for 16S and 18S.

If you are looking for a full tutorial on 18S data, you could consider this:

QIIME2 snakemake workflow tutorial - 18S/16S tag-sequencing

Tutorial: Run qiime2 for 18S or 16S tag-sequencing using snakemake Sarah Hu Summary: This tutorial was written with qiime2-2019.4 for 18S tag-sequencing (but can be adopted for any metabarcoding. Below tutorial uses an 18S dataset to go from raw fastq files to a complete ASV tutorial. I will continue to update this tutorial and add to it on the GitHub repos listed below. Tag-sequencing pipeline to generate ASVs - https://github.com/shu251/tagseq-qiime2-snakemake - input raw fastq sequences,…

Let us know if you have any questions!
Colin

P.S. I've made this thread public so that other people can help answer questions and new users can find it in the future.