What is GSR database?

GSR database (Greengenes, SILVA, and RDP database) is an integrated and manually curated database for bacterial and archaeal 16S amplicon taxonomy analysis. Unlike previous integration approaches, this database creation pipeline includes a taxonomy unification step to ensure consistency in taxonomical annotations. The database was validated with three mock communities and two real datasets and compared with existing 16S databases such as Greengenes, GTDB, ITGDB, SILVA, RDP, and MetaSquare. Results showed that the GSR database enhances taxonomical annotations of 16S sequences, outperforming current 16S databases at the species level. The GSR database is available for full-length 16S sequences and the most commonly used hypervariable regions: V4, V1-V3, V3-V4, and V3-V5.

Downloading the database

GSR database can be download here: Download database


Usage guidelines and published code is available here: https://github.com/ManichanhLab/GSR-16SDB

Citing GSR database

If you find the GSR database helpful, please cite:

Leidy-Alejandra G. Molano, Sara Vega-Abellaneda, Chaysavanh Manichanh. GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis. mSystems (2024) https://doi.org/10.1128/msystems.00950-23

Contact information

Feel free to contact us if you have any feedback, questions or issues:

Leidy-Alejandra G. Molano: gonmola@hotmail.es
Sara Vega-Abellaneda: saravg99@gmail.com
Chaysavanh Manichanh: cmanicha@gmail.com

GSR-DB by Leidy-Alejandra G. Molano, Sara Vega-Abellaneda, Chaysavanh Manichanh is licensed under CC BY-NC 4.0