Qiime vs illumina basespace 16s pipeline, Which is better?

[illuminaGA]

Hello everyone, we currently handle a 16 project which analyzed by QIime and illumina basespace 16s app. The results are quite different. I googled and didn't find any information about comparing those two pipelines.

For now, we found out that the reference(GG vs sliva) and similarity(99 vs 97) are different.

I am wondering that if someone had experience about those two pipelines could give me some pointers about other parameters of something else may cause the differents and how to troubleshoot.

Thank you in advance.

[thermophile]

I've only used the Illumina pipeline once (for that matter I prefer mothur to qiime). The Illumina pipeline is a total black box, do you trust every decision they made for you but didn't document? When I used it, it seemed to just be a taxonomic matching against a database (blast? maybe) rather than OTU based

Check out the mothur miseq SOP for guidelines. Feel free to use my batch file which is based on that SOP https://github.com/krmaas/bioinforma...r/mothur.batch

[illuminaGA]

I've only used the Illumina pipeline once (for that matter I prefer mothur to qiime). The Illumina pipeline is a total black box, do you trust every decision they made for you but didn't document? When I used it, it seemed to just be a taxonomic matching against a database (blast? maybe) rather than OTU based

Check out the mothur miseq SOP for guidelines. Feel free to use my batch file which is based on that SOP https://github.com/krmaas/bioinforma...r/mothur.batch

Thank you so much.

Is the mothur the best pipeline currently?

[thermophile]

Is the Atlantic ocean the best ocean? I don't think best exists.


I prefer mothur because it is very transparent with methods used and simple to install on any OS (there are a few scientific reasons I like mothur related to clustering 16s based on alignment rather than pairwise but qiime has incorporated most of those these days). I also don't like "pipelines" because that seems to be code for people who don't want to go through the bother of understanding how their sequences are processed.