Preparing SILVA 138 rep seqs

[HIROSUKE]

Hi,

I would like to make 97% and 99% OTU data sets derived from SILVA 138 data for using “feature-classifier fit-classifier-naive-bayes” command. How should I do to make the OTU data sets? Shoud I use any other tools to align and annotate the sequences?

[SoilRotifer (Mike Robeson)]

Hi @HIROSUKE,

We'll have some more news about this near the end of the month. For now, please take a look at this and other related SILVA 138 related forum threads:

SILVA 138 Classifiers

This pipeline has been vastly improved via the new RESCRIPt plugin. Which you can check out via the link below. We hope the process of constructing your own reference sequence database (e.g. SILVA) will be far less onerous.

Click here to see the original documentation

I just wanted to let everyone be aware that I've hobbled together a simple <a href="https://github.com/mikerobeson/make_SILVA_db">pipeline</a> for constructing classifiers based …

Also, there is no need to make a 97% classifier, unless you are limited by memory and storage space.

-Mike