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Are you interested to assemble an animal, plant, or fungal genome? Do you already have HiFi, Hi-C, Bionano or parental Illumina data but don’t know where to start? The new VGP-Galaxy assembly pipeline, just published in the nature biotechnology journal, is your answer to these questions! This pipeline, the result of a collaboration between the Vertebrate Genomes Project (VGP) and ERGA, can help you integrate complementary sequencing technologies to generate the most complete and accurate reference genome of your species of interest with just a few clicks. Click here for more information on the pipeline workflows, description and instructions on how to use them. Publication: https://doi.org/10.1038/s41587-023-02100-3

Join us for the first ERGA BioGenome Analyis & Applications Seminar of 2024 featuring a talk by Stein Aerts Wednesday, January 24th - 11:00 CET Link to the Livestream: Modeling and design of cell type specific enhancers using single-cell multi-omics and deep learning Stein Aerts, Professor at University of Leuven; VIB Scientific Director & Group Leader Single-cell transcriptomics and single-cell epigenomics allow building cell atlases of any tissue and species, providing new opportunities to predict gene regulatory networks that control the identity of cell types and cell states. I will present new computational strategies that take advantage of the joint analysis of scRNA-seq and scATAC-seq data, and that derive “enhancer-GRNs” (eGRN) with key transcription factors, genomic enhancers, and predicted target genes per cell type. In parallel, we use deep learning on the scATAC-seq topics to prioritize enhancers and decipher their regulatory grammar. I will discuss the results of several case studies where we applied these computational strategies, including the Drosophila brain and the mouse liver, and I will illustrate how evolutionary comparisons contribute to learning the gene regulatory code in the vertebrate brain. Finally, I will discuss how enhancer models based on deep learning can be exploited to design synthetic enhancers for Drosophila and human cell types.

Join us for the 4th session of the ERGA BioGenome Analyis & Applications Seminars! Wednesday, December 20th - 12:00 CEST Abstracts Speakers Vitor C. Sousa I conducted my Ph.D. at the Gulbenkian Science Institute (IGC, Oeiras, Portugal) and received my degree from the University of Lisbon in 2010, supervised by Lounès Chikhi and Manuela Coelho. I was then a postdoctoral researcher in Jody Hey’s lab (Rutgers University, New Jersey, USA) from 2010 to 2013, and in Laurent Excoffier’s lab (University of Bern and Swiss Institute of Bioinformatics, Switzerland) from 2013 to 2016. Since 2016 I have been a researcher at cE3c, first as an invited researcher, and from 2017 to 2018 as a Marie Sklodowska-Curie fellow. Since 2020 I am an Assistant Professor at the Department of Animal Biology, University of Lisbon. My research aims at characterising the interplay between demographic processes (e.g. gene flow, bottlenecks, population expansions) and natural selection in the structure and divergence of populations. I am the group leader of the Evolutionary Genetics group at cE3c, working on population genomics, and its applications to speciation, conservation, molecular ecology, and human genetics. João Carvalho I am a master in Evolutionary and Developmental Biology from the University of Lisbon and I am currently finishing a PhD in Biodiversity, Genetics & Evolution, supervised by Vítor C. Sousa of the Evolutionary Genetics group at cE3c and co-supervised by Dr Rui Faria and Dr. Roger Butlin. During my PhD I developed new tools to model and simulate Pool-seq data and combined those tools with an approximate Bayesian computation framework to investigate scenarios of ecotype formation.

The ERGA BioGenome Analysis and Applications Seminars represent a joint endeavor of the ERGA Data Analysis Committee (DAC) and the Biodiversity Genomics Europe Work Package 11 - Genome Applications. The purpose of this seminar series is to promote knowledge exchange on state-of-the-art genomic analyses and applications and to create a space for connection and analysis-oriented discussion for ERGA members and the broader genomics research community. These seminars provide opportunities for interdisciplinary interactions that explore emerging scientific trends, providing a platform for cutting-edge research, novel ideas, and insightful discussions. The series will promote an exciting agenda of talks and hands-on sessions on phylogenomics, comparative genomics, population genomics, and functional genomics. When? The seminars happen every month. Check the ERGA Calendar for more information on the upcoming sessions! All seminars will be broadcast on the ERGA YouTube channel. Watch previous sessions:

The new executive board has been elected by the Council! The team brings together six highly engaged researchers that have been active in various ERGA committees and initiatives. We congratulate each one and wish them the best for their new roles and a term full of exciting achievements and opportunities. We look forward to working together under their leadership and vision so that ERGA can advance and accomplish even more! The second ever iteration of "ERGA elections" has been successfully concluded, representing a major step in the efforts to formalise our community. As Camila Mazzoni, ERGA’s founding chair, puts it: “The Phase 1 of ERGA has established the foundation of the network and is currently undergoing consolidation with the support of the BGE Project until its completion. It is now time to initiate Phase 2, during which ERGA will actively promote the scaling up of reference genome sequencing for European Biodiversity.” The electoral procedure was approved and followed closely by the ERGA Council, in accordance with the guidelines established by the ERGA governance Document. The process also received crucial support and oversight from the Nominations Working Group chaired by Alice Mouton, the Elections Supporting Team (Christian de Guttry, Diego de Panis and João Pimenta) and the JEDI Subcommittee. The expanded structure of the executive board draws upon lessons learned during ERGA's first phase. “The newly expanded Executive Board will play a pivotal role in 1) expanding the network of partnerships and projects under the ERGA umbrella, and 2) expanding ERGA’s role as a knowledge hub that supports capacity building across Europe and ensures that genomes sequenced throughout Europe meet the required standards of the Earth BioGenome Project”, explains former chair Camila Mazzoni, “I am delighted to see the ongoing enthusiasm of our members and extend my best wishes to the new Executive Board for success in their mission to steer ERGA into Phase 2.” Learn more about each of the Executive Board roles: Playlist - ERGA Executive Board Phase 2

We are happy to invite you to the ERGA session during the Biodiversity Genomics Conference 2023! BG23 is an online, open conference and free to attend. This year the conference is organized by the Wellcome Sanger Institute Tree of Life programme and Biodiversity Genomics Europe. ERGA will be hosting a session on Friday, October 6th from 14:00 to 16:00 CEST. 📅 Add the session to your calendar! The first hour will be focused on the ERGA community, and some of the committees will give brief presentations about the innovations and resources they are developing; The second hour will include invited scientific talks by ERGA members showcasing the importance of reference genomes to enhance our understanding of European biodiversity. Check the programme below: Check the Abstracts! Watch all the talks:

By Luísa Marins (for Biodiversity Genomics Europe) One of the main goals of BGE is to support the new generation of researchers in biodiversity genomics by promoting training and knowledge sharing activities across Europe. Well-qualified trainers and training materials are essential assets to achieve this objective. Representatives of many BGE partners institutions met last week at the Aristotle University Thessaloniki, Greece, for an intensive workshop focused on developing a foundational training framework in biodiversity genomics. The workshop also aimed at aligning activities and sharing knowledge between the reference-genomes and reference-barcodes communities of BGE. The sessions were distributed across 3 days of theoretical presentations and hands-on activities, covering major steps of the genomic workflow. This journey included everything from sample collection and DNA extraction in the “wet lab” to the final stages of data processing and uploading to computational databases. This very productive workshop was just the start of the broader BGE Joint Network Training task. The valuable insights and lessons learned in Thessaloniki are now being summarised into a handbook. These guidelines will serve as a basis for similar workshops to be organised by other BGE partner institutions across Europe throughout 2024. BGE’s effort to connect expertise from the DNA barcode and full genome strands in joint actions is focused on priority areas in biodiversity research, training, and conservation where current challenges are recognised and there are clear needs for well-aligned developments that will accelerate future work. Stay tuned while we continue our endeavour to demonstrate the benefits of working together!

This call is now closed Are you interested in producing a genome in collaboration with the Biodiversity Genomics Europe Project and ERGA? A new call for species proposals & sampling by the European community is now open! Suggested species will undergo a thorough evaluation process and a number of species will be selected for sequencing based on the process established by ERGA's Sampling & Sample Processing Committee.