Create plant_genomics_assembly (#663)

* Create plant_genomics_assembly

* Update pages/tool_assembly/plant_genomics_assembly

Co-authored-by: Korbinian Bösl <[email protected]>

pages/tool_assembly/plant_genomics_assembly

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+---
+title: Plant Genomics Assembly
+contributors: [Anne Françoise Adam Blondon, Cyril Pommier, Daniel Faria, Paulette Lieby, Sebastian Beier]
+summary: Tool assembly for managing plant genomic data
+tags: [plants]
+page_tag: plant_geno_assembly
+---
+
+## 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?
+<!--- TODO: Add figure --->
+
+### Metadata collection and tracking
+Accurate [documentation](metadata_management.html) of the plant biological materials and samples is critical for interoperability, and should comply with the [MIAPPE](https://www.miappe.org/) standard.
+This information should be submitted to [BioSamples](https://www.ebi.ac.uk/biosamples/), with MIAPPE compliance validated using BioSamples' [plant-miappe.json](https://github.com/EBIBioSamples/biosamples-v4/blob/biohackathon_miappe_checklist/webapps/core/src/main/resources/schemas/certification/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](https://www.ebi.ac.uk/ena/browser/home) (ENA) or of genotyping data to the [European Variation Archive](https://www.ebi.ac.uk/eva/) (EVA).
+[e!DAL-PGP](https://edal-pgp.ipk-gatersleben.de/) 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](https://plants.ensembl.org/index.html), 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](https://www.ebi.ac.uk/ena/browser/view/ERC000020),  whereas plant genotyping data should be submitted to EVA.
+Additionally, data can also be published in e!DAL-PGP.
+
+## Tools used within the tool assembly?
+
+{% include toollist.html tag="plant_geno_assembly" %}