Ruegeria pomeroyi digital microbe databases
Description
These databases consolidate a variety of datasets related to the model organism Ruegeria pomeroyi DSS-3. The data were primarily generated by members of the Moran Lab at the University of Georgia, and put together in this format using anvi'o v7.1-dev through the collaborative efforts of Zac Cooper and Iva Veseli (special thanks to Christa Smith and Lidimarie Trujillo Rodriguez for their help with gene annotations). The data includes:
- (R_POM_DSS3-contigs.db) the complete genome and megaplasmid sequence of R. pomeroyi, along with highly-curated gene annotations established by the Moran Lab and automatically-generated annotations from NCBI COGs, KEGG KOfam/BRITE, Pfams, and anvi'o single-copy core gene sets.
- (PROFILE-VER_01.db) read-mapping data from multiple transcriptome and metatranscriptome samples generated by the Moran lab to the R. pomeroyi genome. Some coverage data is stored in the AUXILIARY-DATA.db file. This data can be visualized using anvi-interactive. Publicly-available samples are labeled with their SRA accession number.
- (R_pom_reproducible_workflow.md) a reproducible workflow describing how the databases were generated.
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