Misc. Important Topics related to Qiime2

First of all Congratulations to all of you for the New Release!!! I am excited.

I started learning and using Qiime 2 not too long ago (approx. 4-5 months) for analyzing 16S amplicon sequencing data (cyanobacteria associated microbiome). I have the following questions related to the analysis:

  • Script to analyze the core microbiome per specimen/ per species in qimme 2
  • Script to follow - in order to remove the sequences of the host species qiime 2
  • How to do the network analysis in qiime 2? (the specific script to follow?)

I would really appreciate your help in this matter. Please let me know if more information is needed.

Thank you

Kind Regards,

Hello Falguni,

Welcome back to the forums! :qiime2:

core-features: Identify core features in table — QIIME 2 2019.10.0 documentation :bouquet:

Maybe check out the quality control plugin and the filtering used by the deblur plugin.

Did you search the forums for "network"? I found the q2-SCNIC tutorial and I think that is what you are looking for.


1 Like

I just want to mention that Im not sure q2-SCNIC is supported past the 2018.11 release. (I haven’t gotten it to work with more recent updates). Its a little bit finicky to get to work, but Ive gotten some really nice networks out of it.



This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.