BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.

Alneberg J, Sundh J, Bennke C, Beier S, Lundin D, Hugerth LW, Pinhassi J, Kisand V, Riemann L, Jürgens K, Labrenz M, Andersson AF

Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]

The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

Bioinformatics Support for Computational Resources [Service]

NGI Stockholm (Genomics Applications) [Service]

NGI Stockholm (Genomics Production) [Service]

National Genomics Infrastructure [Service]

PubMed 30063227

DOI 10.1038/sdata.2018.146

Crossref 10.1038/sdata.2018.146

pii: sdata2018146
pmc: PMC6067050
European Nucleotide Archive: PRJEB22997 https://www.ebi.ac.uk/ena/data/view/PRJEB22997
SRA: SRP058493 https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP058493
BARM Annotation and Quantification Data
SRA: SRP077551 https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP077551