Hi team, I have to analyze NGS data of 11 samples performed in Illumina MiSeq targeting the V1-V3 region of 16S rRNA, I have received the FASTAQ files of each sample (trimmed Fw and Rv and merged), I am thinking to use QIIME 2 for further downstream processing. Since I am completely naive to NGS data analysis I would love to hear your expert suggestions about the pipeline for analyzing those data for microbiome composition. Should I use QIIME2 using virtual box? It would be a great help for me if I could hear your advice, just watched your very informative tutorial "importing and demultiplexing". Thanks so much for your great support,
Hi @Microbiome, thanks for your question and welcome to the forum!
The exact pipeline you use will depend on the question you are trying to answer, and there are several tutorials available that might be appropriate. The Parkinson’s Mouse Tutorial is a great place to start, but it sounds like your data might have already been partly processed and might need to be imported differently. The Importing data tutorial can help with that.
Regarding installation, the answer is "that depends" as well, I'm afraid. VirtualBox is considered a "backup option" in the docs, and there are a number of native install options depending on your OS and available hardware.
I'm at UNSW too (in Canberra), and I am happy to chat on Teams if you need more direct support (I'm Benjamin Kaehler). Good luck, and let us know how you go!