Online 16S rRNA gene classification

Question

[mikael.lenz.strube]

Hi all,

I'm looking for at easy-to-use 16s pipeline for teaching purposes. It is much to complicated in this particular wet lab course to do the whole command line story, and it sort of misses out on some teaching points to just hand them the analysed data.

I was looking at the RDP pipeline which i think would do the trick, but do any of you have other suggestions? Ideally somethin that takes a pair of illumina files and eventually returns an abundance table or similar.

[andres.firrincieli]

I would look at qiime2-dada2. There are several online tutorials that explains step-by-step how to process Illumina libraries and obtain an abundance table: Tutorial 1; Tutorial 2; Tutorial 3. These tutorial returns an abundance table of Amplicon Sequence Variants

An alternative would be the Mothur-MiSeq pipeline; here the sequences are clustered into 97% OTUs

[mikael.lenz.strube]

This unfortunately requires command line and a bunch of downloading, which is beyond the scope of the course. I think i will use the galaxy framework.

[andres.firrincieli]

I completely missed that. Good luck with your course!

Answer 1

[gb]

What about galaxy?

https://usegalaxy.org/

https://galaxyproject.org/

[GenoMax]

Direct link to Galaxy tutorial:
https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html

[mikael.lenz.strube]

Perfect, completely forgot about galaxy. Thank you!

[gb]

To add: I thought I have seen that there is a possibility that you can get a private galaxy environment for teaching purposes for free (temporary of course). But for now I am now sure anymore because I can not find it anymore.