Misc. Important Topics related to Qiime2

[fpaul015 (Falguni Paul)]

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,

[colinbrislawn (Colin J Brislawn)]

Hello Falguni,

Welcome back to the forums!

@fpaul015

• Script to analyze the core microbiome per specimen/ per species in qimme 2

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

@fpaul015

• Script to follow - in order to remove the sequences of the host species qiime 2

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

@fpaul015

• How to do the network analysis in qiime 2? (the specific script to follow?)

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

Colin

[jwdebelius (Justine Debelius)]

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.

Best,
Justine