Search Results

The European Reference Genome Atlas ( ERGA ) and the European node of the International Barcode of Life ( iBOL Europe ), two international communities of scientists brought together under the Biodiversity Genomics Europe  Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics  and the intersection of their communities. In our previous posts, we compared DNA to a book: barcodes help us identify which book we are holding, while reference genomes enable us to read every page. But here is the twist: by the time DNA leaves the wet lab, the book is broken as if we have run the pages through a “paper–shredder”. DNA extraction, library preparation, and DNA sequencing all turn the long DNA sequence into millions of pieces (Check the Connections blog #3  for an overview of these different steps of the genomic workflow). Bioinformatics is the art of turning that pile of shreds back into something we can read, search, and compare. It is the art that turns barcodes and reference genomes into usable knowledge. Figure 1: Informatics and advanced computing are necessary to analyse the huge amount of data generated for genomic research. Bioinformatics is the product of molecular biology meeting computing. Bioinformatics facilitated the development of the first sequence alignments and substitution matrices, dynamic programming, the creation of searchable databases, and the first “find-it-fast” tools that supercharged homology searches. As sequencing scaled, assembly algorithms emerged, followed by hybrid approaches for long-read platforms. Alongside the algorithms came various file formats (FASTA/FASTQ/BAM/CRAM/GFF/GTF), workflow engines, and the hard-won lesson that reproducibility matters more than quick fixes. For barcoding, the task is targeted: extract a standard marker (or “abstract”), check its quality, align it against a trusted database, and report the most accurate match with confidence. Think of well-indexed catalogues and fast look-ups, ideal for monitoring and quick assessments. For reference genomes, the task is editorial. Correct sequencing errors, assemble the million pieces into chromosomes, phase haplotypes, polish with multiple evidence tracks (long reads, linked reads, Hi-C, RNA-seq), and annotate genes and repeats. That finished “book” enables population genomics, local adaptation, and conservation genomics studies. Figure 2: Examples of some common bioinformatics tasks when working with genomic data from across the tree of life. Bioinformatics is the art that turns raw data into knowledge with useful applications for biodiversity. Modern analyses involve dozens of steps, quality checks, trimming, deduplication, mapping, variant calling, assembly, scaffolding, annotation, all wrapped in containers and workflows to make sure a colleague can re-run them on Tuesday and get an answer on the same day. Good metadata is the structure that holds all the pages: sample, permit, locality, preservation, instrument, kit, and version numbers (Check this episode of the Genomic Connections Podcast  to learn more about the importance of metadata). Without that structure, even the finest assembly becomes a vague curiosity. A few field notes from the trenches Everyone has a story of a 2 a.m. run that failed because a file was called final_FINAL_reallyFinal.fastq.gz. We have all been rescued by checksums, saved by containerised toolchains, and learned never to delete intermediate files before the multi-QC report is green. We name scripts after pets, we comment our code (eventually), and we celebrate the day a 500 GB BAM shrinks elegantly into a reproducible VCF. Why does this matter to BGE? For iBOL Europe, robust bioinformatics means clean barcode libraries, sound assignments, and credible trend analyses. For ERGA, it means reference genomes that stand up to re-analysis and can power subsequent population, functional, and comparative genomics, the applications stakeholders care about (from conservation planning to bioeconomy uses). Bioinformatics is not an afterthought: it is a research field itself! It is the bridge from sequencer output to decisions. Treat pipelines as publishable methods, treat metadata as data, and treat your future self as a collaborator who deserves clarity. In the next post, we will demonstrate how these computational foundations are applied in practical settings, including monitoring, policy, and management, without losing sight of the overall context (or the pages).

Last week, ERGA was present at the Vertebrate Genomes Project 2025 Conference , held at The Rockefeller University in New York City from September 30 and October 1. ERGA and VGP share a long-standing collaboration, working together on shared workflows for genome assembly and evaluation  and collaborating under the Biodiversity Genomics Project ( BGE ). So far, dozens of vertebrate genomes from species found across Europe have been sequenced under the ERGA umbrella, directly contributing to the VGP’s goal of sequencing all ~70,000 living vertebrate species. Discussing vertebrate genomes in the heart of New York City. Tom Brown, coordinator of the ERGA IT & Infrastructure Committee , presented the work within the BGE project on FAIR (Findable, Accessible, Interoperable, and Reusable) genome assembly publishing and establishing distributed models of genome generation across Europe. As the VGP and the Earth BioGenome Project (EBP) begin their journey into the Phase II expansions of each project, attention must be given to fully FAIR reporting and publishing of all outputs from sample to reference genome, and coordinated across all nodes of the EBP.  In New York, Tom presented ERGA’s solutions for  generating reports  for all genomes produced as part of the BGE project and sharing all bioinformatic workflows within WorkflowHub . Photos by Chul Lee . Relevant links VGP Website: https://vertebrategenomesproject.org/ Larivière, D., Abueg, L., Brajuka, N. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol 42 , 367–370 (2024). https://doi.org/10.1038/s41587-023-02100-3

29–31 October 2025 Summary 🗓️ Dates:  29 - 31 October 2025 ( click to add to your agenda! ) 🔗 Online venue: ERGA YouTube Channel We are excited to announce the Genomics for Biodiversity Conference  organised by ERGA-BGE, which will be held on October 29 - 31 and transmitted live through the ERGA YouTube channel . Participation is free of charge. ✉️ Click to sign up & receive event updates in your inbox! The event aims to bring together researchers and other stakeholders interested in applied biodiversity genomics and will showcase how it can have an impact on real-world issues, focusing primarily on biodiversity conservation and the bioeconomy.   Programme Through two and a half days, the conference will include: Keynote talks  - addressing the links between biodiversity genomics, policy, and society. 29 Genomic for biodiversity projects presentations  - they will showcase the applied use of biodiversity genomics across Europe and a diverse set of eukaryotic species.  Click here to learn more about the projects. 3 sessions focusing on genomics applied to biodiversity conservation and standardisation. ERGA-BGE Case Studies The Biodiversity Genomics Europe Project and ERGA have supported 29 research projects that demonstrate the applications of genomic data to improve our understanding of biodiversity. In this conference, research project participants will have a chance to come together, share scientific results, and exchange experiences. Learn more about the projects in the interactive map below: Parallel sessions On Friday, 31 October 2025 (11:30–13:00 CET), three parallel breakout sessions, Conservation Genomics, Bioeconomy Genomics, and Genomic Data Standardisation , will run concurrently. Each session will include selected flash talks on genomics‑driven study that fits one of the three themes and can be communicated clearly within a timed and visually engaging five‑minute presentation: Genomics for species monitoring and management Genomics techniques for conservation Standardization in genomics The abstract submission deadline is September 15th. Selected speakers will be notified by October 7th.  The Biodiversity Genomics Europe ( BGE ) Project is funded by the European Union's Horizon Food, Bioeconomy Natural Resources, Agriculture and Environment Framework Programme Additional support:

citizenscience@erga-biodiversity.eu < Back CS - Citizen Science citizenscience@erga-biodiversity.eu The Citizen Science and Outreach Committee aims to facilitate collaboration and communication between scientists, stakeholders and citizens to increase trust in the scientific process and ensure that genomics research reflects the needs and perspectives of the broader community. By engaging a broad range of stakeholders, including policy makers, non-governmental organisations, industry representatives and citizens, the Committee seeks to foster a fruitful multi-stakeholder dialogue and support the traditional community knowledge through the use of citizen science and stakeholder perspectives. To achieve its goals, the Committee works to engage citizens and stakeholders in the research process and to promote public understanding of genomics through various public events and other activities. In addition, the Committee supports policies that support genomics research and its translation into practical applications for the benefit of society. (V.1.0 02.05.2023) Chair Elena Buzan Coordinators Christian de Guttry Luísa Marins Steering Committee Jacob Höglund Lino Ometto Svein-Ole Mikalsen Chiara Bortoluzzi Connection #7 - Citizen science, allies, definitions, and common misconceptions Press Releases A colorful genome: meet the rare Mediterranean White-spotted Yellow Wart Slug Press Releases Genomics for Biodiversity Conference - from genomes to impact Press Releases

ERGA Library Filter by Category Select Category Publication Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation Year: 2025 DOI/URL: https://onlinelibrary.wiley.com/doi/10.1111/mec.70001 Next Publication A chromosome-level genome assembly of the European green toad (Bufotes viridis) Year: 2025 DOI/URL: https://doi.org/10.1093/g3journal/jkaf002 Next Publication Chromosome-level reference genome assembly for the mountain hare (Lepus timidus) Year: 2025 DOI/URL: https://peercommunityjournal.org/articles/10.24072/pcjournal.514/ Next Publication The genome sequence of the Violet Copper, Lycaena helle (Denis & Schiffermüller, 1775) Year: 2025 DOI/URL: https://doi.org/10.12688/f1000research.156485.1 Next Publication Nuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium Year: 2025 DOI/URL: https://doi.org/10.1093/gbe/evaf003 Next Publication Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis Year: 2024 DOI/URL: https://doi.org/10.1038/s41597-024-04222-y Next Publication A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00068-0 Next Publication The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00054-6 Next Publication Building a Portuguese coalition for biodiversity genomics Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00061-7 Next Publication Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00053-7 Next Publication First Chromosome-Level Genome Assembly of a Ribbon Worm from the Hoplonemertea Clade, Emplectonema gracile, and Its Structural Annotation Year: 2024 DOI/URL: https://doi.org/10.1093/gbe/evae127 (Funded by the Research Council of Norway project “InvertOmics—phylogeny and evolution of lophotrochozoan invertebrates based on genomic data” (project number: 300587 to T.H.S.) Next Publication The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion Year: 2024 DOI/URL: https://doi.org/10.1038/s41437-024-00720-2 Next 1 2 3 1 ... 1 2 3 ... 3

OUR PARTNER PROJECTS ERGA is the pan-European partner of the Earth Biogenome Project (EBP) Regional Partners: French Atlas of Marine Genomes (ATLASea) Earth Biogenome Project Norge (EBP-Nor) Swedish Earth BioGenome Project Worldwide Partners: