Soil Microbe Database (SMDB) - a whole-genome reference database with over 50,000 genomes, focused on soil biodiversity
Includes over 20,000 metagenome-assembled genomes (MAGs) from soils, and 1400 fungi from Joint Genome Institute's Mycocosm
For full details and genome sources, check out our preprint (coming soon)!
Explore/download abundances of each genome across NEON soil samples using the interactive portal, developed in partnership with the Boston University Software & Application Innovation Lab (SAIL) (coming soon)!
For local classification against metagenome samples, the database files can be downloaded, along with Snakemake rules for each step of classification (Kraken2 for read classification, Architeuthis for kmer-filtering, and Bracken for abundance estimation)
To add genomes to the database, you will need to download the Struo2 software and have the filepaths of local genomes, along with their NCBI taxonomy
The National Ecological Observatory Network is a project solely funded by the National Science Foundation and managed under cooperative agreement by Battelle. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Information and documents contained within this repository are available as-is. Codes or documents, or their use, may not be supported or maintained under any program or service and may not be compatible with data currently available from the NEON Data Portal.