Anyone knows the workflow/software needed in order to compare different FASTQ files?

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António GG Sousa

Hi,

For downstream analysis, i.e., community comparisons, I recommend you the phyloseq R package (Article Phyloseq: An R Package for Reproducible Interactive Analysis...

). You can also use the widely used QIIME (http://qiime.org) and mothur (https://www.mothur.org) softwares that in my opinion are more suitable to upstream analysis (filtering, clustering, taxonomic assignment) than downstream (diversity). In my opinion, among these two, QIIME produces better plots and graphics to visualize that are more suitable to publish. In any cases, you will need to be careful when convert your (I guess!) OTU table with taxonomy to any of these softwares, inclusive the phyloseq R package.

I hope it helps.

Best Regards,

António