Perceived Issues with them
I have been informed of the following by their users:
- They do not provide a download link for CSV files. Users have had to email support. They received an Excel file (which can then be saved as a Tab-limited text file which may be uploaded).
- The FastQ files from them are atypical and at present cannot be used for alternative-analysis thru BiomeSight or Thryve.
- They do not provide NCBI Taxon numbers, only names (which cannot all be matched to NCBI names).
- They do not provide rollup numbers to higher level of taxonomy ranks. In fact, their numbers total 100% identification. This is misleading because there are bacteria that still cannot be identified and other processors often report 5-10% unknown bacteria.
Thanks to an open source project, I managed to get over 99% reliable matching to NCBI Taxon numbers on test samples. I also generate rollups to higher taxonomy rank from their “bottom” level numbers using the NCBI hierarchy.
I prefer the lab to own both the NCBI taxonomy numbers and the rollups — they can be gotchas with appropriate interpretations and they are the people that should know best.