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Plant Genomics Assembly Edit me

Tool assembly for managing plant genomic data

What is the plant genomics tool assembly?

The plant genomics tool assembly is a toolkit for the management of plant genomics and genotyping data throughout its lifecycle, with a particular focus on ensuring traceability of the biological materials to enable interoperability with plant phenotyping data.

Who can use the plant genomics tool assembly?

This tool assembly can be used by any researcher producing plant genomic or genotyping data interested in ensuring their data complies with the FAIR principles.

How can you access the plant genomics tool assembly?

All the components of this tool assembly are publicly available, but most require registration. So anyone can access the tool assembly provided they register for each tool that requires it.

For what purpose can you use the plant genomics tool assembly?

Tools and resources used in managing plant genomics and genotyping data.
Figure 1. The plant genomics tool assembly.

Metadata collection and tracking

Accurate documentation of the plant biological materials and samples is critical for interoperability, and should comply with the MIAPPE standard. This information should be submitted to BioSamples, with MIAPPE compliance validated using BioSamples’ plant-miappe.json template. Submission of sample descriptions to BioSamples can be done as early as the data collection stage, but at the latest, must acompany submission of the genomic data to the European Nucleotide Archive (ENA) or of genotyping data to the European Variation Archive (EVA). e!DAL-PGP can be used to manage and share experimental metadata, as well as data.

Data processing and analysis

Reference genomes for genome assembly and annotation should be obtained from ENSEMBL Plants, if available. Genetic variant data must be produced in the VCF format, and validated using the EVA vcf-validator (https://github.com/EBIvariation/vcf-validator).

Data sharing and publishing

Plant genomic data should be submitted to ENA together with metadata compliant to the GSC MIxS plant associated checklist, whereas plant genotyping data should be submitted to EVA. Additionally, data can also be published in e!DAL-PGP.

More information

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Relevant tools and resources

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Tool or resource Description Related pages Registry
BioSamples BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Documentation and metadata Plant sciences bio.tools TeSS
e!DAL-PGP Plant Genomics and Phenomics Research Data Repository Plant sciences Researcher Data steward research Data steward infrastructure FAIRsharing
Ensembl Plants Open-access database of full genomes of plant species. FAIRsharing TeSS
European Nucleotide Archive (ENA) A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation Microbial biotechnology bio.tools FAIRsharing TeSS
European Variation Archive (EVA) Open-access database of all types of genetic variation data from all species. bio.tools FAIRsharing
MIAPPE Minimum Information About a Plant Phenotyping Experiment Documentation and metadata Researcher Data steward research Plant sciences FAIRsharing TeSS
MIxS Minimum Information about any (x) Sequence Documentation and metadata Researcher Data steward research Marine metagenomics FAIRsharing TeSS