Dear all,
I am performing analysis of 16S rRNA amplicon sequencing data. I have tested effectivity of two classifiers on the mock community and blast classifier shows the best result. However, I found out blast is using a local sequencing alignment. So I do not know if it is appropriate to use this classifier to assign a "mystery" sequence to a bacterial taxon. Is it possible that this approach will result to false positive results? Is it better to use Vsearch classifier which showed worse results but is using a global sequencing alignment?
And a bonus question. Should I use rarefied representative sequences to perform a taxonomy classification or not? I use rarefied data for alpha diversity testing (and for beta diversity testing I do not).
Thank you all for answers!
Martin
Article To rarefy or not to rarefy: robustness and efficiency trade-...
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