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, Sam Miller, 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. It also contains annotations for the Moran Lab's TnSeq mutant library.
- (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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