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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
KTH Royal Institute of Technology.
Stockholm University.
Leibniz Inst Balt Sea Res Warnemunde, Germany.
Leibniz Inst Balt Sea Res Warnemunde, Germany.
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2018 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed) Published
Abstract [en]

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. [GRAPHICS] .

Place, publisher, year, edition, pages
Nature Publishing Group, 2018. Vol. 5, article id 180146
National Category
Bioinformatics and Systems Biology
Research subject
Ecology, Microbiology
Identifiers
URN: urn:nbn:se:lnu:diva-77392DOI: 10.1038/sdata.2018.146ISI: 000440291200001PubMedID: 30063227OAI: oai:DiVA.org:lnu-77392DiVA, id: diva2:1242917
Available from: 2018-08-29 Created: 2018-08-29 Last updated: 2018-10-24Bibliographically approved

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Lundin, DanielPinhassi, JaroneRiemann, Lasse
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