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Norwegian data management tool assembly for marine metagenomics data

What is the Norwegian tool assembly for marine metagenomics data management?

The Norwegian tool assembly for marine metagenomics aims to provide a comprehensive toolkit for management of marine genomic research data throughout a project’s data life cycle. The toolkit, developed by students and researchers in Norway, contains resources and software tools for both data management (Planning, Processing, Storing and Sharing), data analysis and training. It is built on the Norwegian e-Infrastructure for Life Sciences (NeLS) tool assembly of ELIXIR Norway and the Marine Metagenomics Platform (MMP).

Who can use the marine metagenomics data management tool assembly?

This tool assembly is useful for students and researchers in Norway who are interested in analysing marine datasets (e.g. genomes and metagenomes and transcriptomes). Parts of the assembly, such as data storage, are based on national infrastructures, laws and regulations, and consequently limited to Norwegian users, while other parts, such as data analysis tools and data repositories, are globally accessible.

How can you access the marine metagenomics data management tool assembly?

To be able to use resources and tools that are mentioned here, you are recommended to have a Feide account. In addition, it is important for you to have a NeLs account in order to access usegalaxy.no. In case your institution does not use the national Feide secure login service, you can apply for a NeLs IDP through the ELIXIR Norway help desk. Note, that Marine Metagenomics Platform (MMP) is an open-access platform that can be accessed without a FEIDE account at https://mmp2.sfb.uit.no/.

For what purpose can you use the marine metagenomics data management tool assembly?

Diagram on tools in the Data Life Cycle in the Marine Metagenomics tool assembly.
Figure 1. The Marine Metagenomics data management tool assembly.

Data management planning

The support for data management planning for marine metagenomics in Norway is provided through the ELIXIR-NO instance of the Data Stewardship Wizard. You can access the Data Management Plan model for marine metagenomics in Norway here. Read more on standards and best practices for the metagenomics data life-cycle here. Questions regarding the DSW and data management in general can be directed to the ELIXIR Norway help desk.

Data collection

If you use one of the National Norwegian research infrastructures, such as the Norwegian sequencing infrastructure NorSeq, they can directly upload data to your NeLS project for you, as described in this page

Data storage, sharing and compute

The solutions for data storage, sharing and computation are built on the services and infrastructure delivered by ELIXIR Norway described in the Norwegian e-Infrastructure for Life Sciences (NeLS) tool assembly.

Data processing and analysis

The Marine Metagenomics Portal provides a complete service for analysis of marine metagenomic data through the tool META-pipe. META-pipe is a pipeline that can assemble your high-throughput sequence data, functionally annotate the predicted genes, and taxonomically profile your marine metagenomics samples, helping you to gain insight into the phylogenetic diversity, metabolic and functional potential of environmental communities. You can find more details about META-pipe here. Norwegian users with Feide access can access the online version of META-pipe. For other users META-pipe is downloadable and can easily be run on any computing environment (e.g. any Linux workstation, SLURM cluster or Kubernetes).

Usegalaxy.no is a Norwegian instance of the Galaxy web-based platform for data intensive life science research that provides users with a unified, easy-to-use graphical interface to a host of more than 200 different analysis tools. Here you can find tools for a wide variety of analysis for your marine metagenomic and genomic data. The tools are publicly available in the Galaxy Toolshed which serves as an “appstore” so you can easily transfer them to your favourite Galaxy instance anywhere. You can run the tools interactively, one by one, or combine them into multi-step workflows that can be executed as a single analysis. Premade workflows (i.e for Taxonomic classification of metagenomic sequences) are provided, and you can request installation of your favourite tool by contacting the ELIXIR Norway help desk.

Data sharing and publishing

ELIXIR Norway acts as a broker for Norwegian end-users that wish to submit data to ELIXIR Deposition Databases (such as ENA), providing support in submitting the data on behalf of the data owners directly from the National e-infrastructure for Life Science (NeLS).

If you need help with publishing or are interested in using the brokering service, please contact the ELIXIR Norway help desk.

Data reuse

The Marine Metagenomics Portal (MMP) provides you with high-quality curated and freely accessible microbial genomics and metagenomics resources. Through MMP you can access the The Marine reference databases (MarRef), Marine Genome Database (MarDb), (MarFun), and (SalDB) contextual databases. They are built by aggregating data from a number of publicly available sequence, taxonomy and literature databases in a semi-automatic fashion. Other databases or resources such as bacterial diversity and culture collections databases, web mapping service and ontology databases are used extensively for curation of metadata. At present the MarRef contains nearly 1,000 complete microbial genomes, and MarDB hosts more than 13,000 non-complete genomes. The MAR database entries are cross-referenced with ENA and the World Register of Marine Species (WoRMS). You can read more about the Mar databases here.

More information

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Relevant tools and resources

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Tool or resource Description Related pages Registry
Feide Feide is the national solution for secure login and data exchange in education and research. Feide can be linked with ELIXIR-AAI through eduGAIN. TSD for sensitive data - Norway NeLS assembly
Galaxy Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. NeLS assembly Data analysis Researcher Data steward infrastructure IFB - France bio.tools TeSS
MarDB MarDB includes all non-complete marine microbial genomes regardless of level of completeness. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation. bio.tools
MarFun MarFun is a manually curated marine fungi genome database.
Marine metagenomics portal High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community bio.tools
MarRef MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information bio.tools
Meta-pipe META-pipe is a pipeline for annotation and analysis of marine metagenomics samples, which provides insight into phylogenetic diversity, metabolic and functional potential of environmental communities. Data analysis bio.tools TeSS
NeLS Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data NeLS assembly bio.tools
salDB SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae.