QIIME2 Nanopore 18S full length Amplicon sequenced data analysis

[cherman2 (Chloe Herman)]

Hi @Adyasha_Panda,
18S amplicon studies are not my speciality but my understanding is the workflow is generally very similar to the 16s data. What specifically is not working for you about SILVA 138.2 databases as taxonomy classifier?

Here are so resources from the forum:

18s analysis with Qiime2

Hi @pshtiwan_babane, the approach would be no different than using a typical 16S rRNA gene analysis pipeline. The easiest approach would be to use the SILVA reference database as it contains the Small Sub Unit (SSU) sequences for both the 16S and 18S rRNA genes. QIIME 2 formatted SILVA reference files and classifiers are available on the Data resources page.

https://forum.qiime2.org/t/18s-data-taxonomic-classifiers/17964/10