Dear All, We have done V1-V9 illunima sequencing for our amplicon sequence analysis. Ive executed standard QIIME2 pipeline using GG database. But in qiime2 results, i didnt get any species level information. Hence I tried with kraken2 (ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v1_8GB_201904_UPDATE.tgz) database and GG special database. But the taxonomy which i get from these two database varies dramastically in species level. For example: In NCBI ref seq: The top bacteria in Pseudomonas aeruginosa where as in GG results, Pseudomonas Veronii. Which is authenticated? Kindly Guide me
Dear Monica,
Databases used for the taxonomy annotation have a significant annotation error rate, around 15% and distinct nomenclatures! You can read the paper of Edgar (doi: 10.7717/peerj.5030). Depending on your goal, yous should select a database (RDP?) that will be compatible with the analyses to be followed and be less demanding on the taxonomy level. You can also create your own database.
- Badges
- Science topic
- Similar topics
- Entomology
- Resistance