Hello everyone,
I run a project that consists of over 2,000 fecal samples. This project is ongoing, and the aim is to build a database whereby we can compare the microbial profile of a new sample to the existing average, and add the new sample to the database, and so on.
I currently analyze these samples with a protocol similar to the Fecal Microbiota Transplant (FMT) study tutorial in QIIME2. Each Illumina 16S sequencing run is processed separately, merged following filtering and denoising with DADA2, and then analyzed with core diversity metrics and taxonomic classification (statistics externalized to SAS and R). Right now, our external QIIME2 dedicated server can handle this dataset, however, analysis is becoming time consuming due to file size.
My question is how to build a microbiome database and what steps to take to properly analyze a project of this scale? Can QIIME2 handle something like this in the long run? Do I have to keep re-analyze the entire dataset with each additional run?
I would appreciate any advice or directions to resources to accomplish something like this.
Thank you in advance QIIME2 developers and community! I really appreciate all of your hard work!