I was reading throughout the QIIME 2 manual, and I was wondering if the following train of thought somewhat accurate:
- I first imported my raw Illumina MiSeq data and control data from SRA.
- I joined my reads (here’s where it can get a bit complicated), but I noticed that the SRA data has been previously filtered and merged in QIIME. Would it hurt to rerun this again? Should I just import the SRA data in later steps?
- I applied denoising using Deblur.
- I realized that somewhere in the guide it says that Deblur has somewhat a dechimerization process, but regardless of that I ran Vsearch de-novo chimera search, is this redundant given that Deblur removes some of them?
- I took the output from the non-chimera artifact, and performed a de-novo clustering. (I’m guessing in this part I should have added the SRA sequences)
- I downloaded the rep-set from Silva 16S only with 99 similar sequences, along with the same 99 folder for taxonomy, and I’m running (as I write this) the “Assign taxonomy” function with Vsearch-consensus.
I guess I’m just afraid I’m screwing somehow something by rerunning dechimerization, or re-filtering the filtered data from NCBI. Is multithreading already applied to every process in qiime? Or do we have to set it up in order to maximize all possible cores from our computer?
Thanks for this!