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The ERGA Community Genome Reports Collection - an open platform for the community

The new ERGA Community Genome Reports Collection hosted at Pensoft’s RIO Journal offers an open and inclusive space for Genome Reports produced by the ERGA community. With clear guidelines and a shared platform for creating standardised reports, we hope to reduce the effort required from individual researchers. In doing so, we aim to support the production of more high-quality Genome Reports, increasing visibility, recognition, and reusability across the entire community. The RIO Journal platform allows preprinting at no cost and publishing following a standardised format for an affordable fee. The collection also accepts Genome Reports published elsewhere - so if you wish to publish in a different journal the report can still be displayed in the ERGA collection. More details about the process are outlined below.


Several genome reports are already available in the ERGA Community Genome Reports Collection. 


What is a Genome Report?


  • A Genome Report is a technical publication that describes all the steps taken to produce a reference genome: sampling, sequencing, assembling, annotating.

  • They follow a standardised format and structure that allows readers to quickly and easily understand the quality of the genome and how it was generated.

  • Genome reports are “data papers” - unlike classical research papers, they generally do not include any type of downstream analysis or evolutionary interpretation of results.


A Genome Report will typically include a brief introduction about the species sequenced, a detailed description of the methodology used to obtain the genome (from sampling in the field to the bioinformatic steps) and plots and statistics that summarise the quality of the resulting genome assembly.
A Genome Report will typically include a brief introduction about the species sequenced, a detailed description of the methodology used to obtain the genome (from sampling in the field to the bioinformatic steps) and plots and statistics that summarise the quality of the resulting genome assembly.

Why are Genome Reports encouraged by ERGA?


  • They allow for the proper recognition of everyone who contributed to the production of the reference resource in a citable manner.

  • They support open and reproducible science - by providing all the methodological details that are often cut or condensed in traditional research manuscripts.

  • They allow crucial information to be shared soon after the genome assembly is ready - well before downstream analyses, which can take months or years, are completed. This helps accelerate the use and application of the data.


There are different ways of contributing to the ERGA Community Genome Reports Collection:


[1] Link a Genome Report published elsewhere to the Collection (free of charge)

  • Click on “Add document to collection” ⇒ confirm you have consent of all authors ⇒ import (add) and confirm publication metadata (authors, etc.) ⇒ submit request ⇒ editors check requirements ⇒ accept ⇒ appears in the Collection linked to the source publication

  • No cost


[2] Add a preprint PDF to the Collection (free of charge)

  • Click “Start manuscript” ⇒ confirm you have consent of all authors ⇒ complete publication metadata (authors, abstract, etc.) ⇒ upload your PDF ⇒ submit request ⇒ editors check requirements ⇒ accept ⇒ appears in the Collection as a preprint

  • No cost, Community can comment on the preprint


[3] Write and submit your manuscript for Peer-Review publication in the Collection 

  • Using the ARPHA Platform to create your Genome Report. You can then submit it for peer-review

  • Click “Start manuscript” ⇒ write and submit your manuscript using the ARPHA Writing Tool ⇒ submit request ⇒ editors check requirements ⇒ peer-review ⇒ accept ⇒ appears in the Collection as a peer-reviewed publication 

  • Publication cost: EUR 270 - 330, fully semantically published article with DOI at RIO



What are the requirements for adding a Genome Report to the collection?


The requirements and recommendations for a Genome Report publication to be included in this collection are detailed here. Each submission to the Collection will be evaluated by the Collection Editors, to decide whether the Genome Report satisfies the criteria for inclusion.



Watch this talk by Robert Waterhouse for more details about the collection. If you have any questions about the collection, please contact robert.waterhouse@gmail.com



The creation of this collection was supported by the Biodiversity Genomics Europe (BGE) project through the Horizon Europe Framework Programme of the European Union under grant agreement No. 101059492, funded by Horizon Europe under the Biodiversity, Circular Economy and Environment (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy’s Horizon Europe Guarantee Scheme.


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