Hi guys, I'm trying to perform 16S rRNA data analysis from metagenome sequencing. For which I have installed QIIME. I wonder, what are the softwares or paques base to do analysis for example of quality control, trimming (if it is the case), OTUs, beta, shanon, alpha, and chao indexes, and ploting these results. Please help me. Because when I run esl "print_qiime_config.py -tf", it tells me that I have to install INFERNAL, RAXHPC, USEARCH, MOTHUR among other softwares. All these are necessary?
My dear friend, as previously I recommended you, please go through the software manual before starting to use it. It is everything available in the manual with well explained protocol. Please invest some time to read the content of the following https://docs.qiime2.org/2018.8/install/
I suppose that you are trying to use old, outdated QIIME version.
Please check the second edition of QIIME:
https://docs.qiime2.org/2018.8/
You can easily download ready-to-use virtual machine ISO (e.g. run qiime2 on windows in virtualized linux environment) and you don't need to install any additional software or packages.
What is more, on the website you have very well described packages (modules) included in each step of q2 analysis.
If you have any problem I can help.
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