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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, S-17165 Solna, Sweden..
Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, 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.

Place, publisher, year, edition, pages
Nature Publishing Group , 2018. Vol. 5, article id 180146
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-233290DOI: 10.1038/sdata.2018.146ISI: 000440291200001PubMedID: 30063227Scopus ID: 2-s2.0-85051806706OAI: oai:DiVA.org:kth-233290DiVA, id: diva2:1239392
Funder
Swedish Research Council, 2011-5689Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180816

Available from: 2018-08-16 Created: 2018-08-16 Last updated: 2019-10-09Bibliographically approved

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Alneberg, JohannesHugerth, Luisa W.Riemann, LasseAndersson, Anders F.
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