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Community Guidelines Data & Tools Sampling Resources ERGA Library Media Community Guidelines & Documents ERGA Governance Document The ERGA Governance Document builds on the initial consortium structure guidelines and defines ERGA bodies, procedures, roles, and responsibilities. On registration, ERGA Members agree to be bound by both the ERGA Code of Conduct and this Governance Document . View More Code of Conduct ERGA is a bottom-up, open and inclusive community. ERGA membership is open to any individual who supports ERGA’s objectives, registers as a member, and agrees to be bound by the ERGA Code of Conduct. View More Privacy Policy As a community connecting researchers working in the field of biodiversity genomics, ERGA is committed to protecting privacy and respecting privacy regulations, as outlined in the ERGA Privacy Policy . View More Open Data Policy This document outlines the Open Data Policy (ODP) for ERGA. This includes all data and metadata produced as part of the activities within and/or associated with ERGA. View More ERGA Publication Project Code of Conduct This document sets out concepts, best practices, and expectations for ERGA Members to follow when engaged in collectively developing publication projects that involve the ERGA community. View More ERGA Glossary This page provides explanations about terms and acronyms often used within ERGA and in the context of Biodiversity Genomics. View More Community Guidelines Sampling Resources ERGA Sample Manifest ERGA aims to promote and facilitate ethical and legal sampling practices that are also complete and comprehensive so as to fully document the provenance of all samples. The ERGA Sample Manifest serves as the community standard for documenting sampling. View More Community Interest Species Survey From late 2021 to early 2023 ERGA conducted a community-wide survey to identify species of interest and potential sample providers; the archived list contains ~1700 species of interest. View More sampling-resources Data & Tools ERGA Data Portal Access the Data Portal and Status Tracker here . These resources are developed together with EMBL-EBI and provide the latest information about data available at the European Nucleotide Archive for all species registered under the ERGA umbrella project. View More ERGA Genome Tracking Console (GTC) The purpose of this tool is to facilitate the tracking of samples, sequencing status, assembly and annotation status, and facilitate the deposition of data into the ENA by keeping track of accession numbers. View More ERGA GoaT Page The Genomes on a Tree (GoaT) platform is mantained by the Wellcome Sanger Institute. GoaT helps coordinate efforts across the Earth Biogenome Project (EBP) Network at all stages from planning through sequencing and assembly to publication. View More ERGA GitHub Through community contributions, ERGA is working towards collecting computational workflows, pipelines, and tutorials in the ERGA GitHub Repositories . View More ERGA WorkflowHub Space Through community contributions, ERGA is working towards collecting computational workflows, pipelines, and tutorials in the ERGA WorkflowHub space. View More Galaxy / Genome Assembly View More Structural Annotation Guide A step-by-step guide on how to annotate protein-coding genes in your genome. Developed by the Annotation Committee. View More Guidelines on data submission - ENA This document provides summary of the key steps for submitting raw reads and genome assemblies (including annotations) to the European Nucleotide Archive. Developed by the IT and Infrastructure Committee. View More data-software Media For more information regarding the ERGA brand or other media inquiries please contact us at media@erga-biodiversity.eu. Logo - Transparent PNG ERGA Poster ERGA Banner ERGA YOUTUBE CHANNEL In the ERGA YouTube Channel you will find a number of resources such as recordings of previous seminars, workshops and interviews. Don't forget to subscribe to our channel to stay updated about upcoming events! media-resources ERGA-Consortium Play Video Play Video 04:14 Community-Driven Reference Genomes: Getting to Know Cistus crispus 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video 16:46 Analysing the genomic basis of vectorial capacity and insecticide resistance in Culex species 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video 11:46 From Permits to Samples – An ERGA Community Writing Project How do you turn many individual experiences, workflows, and challenges into something the whole community can use? In this talk, Katja introduces the newly published ERGA SSP paper From Permits to Samples, showing how a large collaborative effort was turned into practical guidance for reference genome generation. https://doi.org/10.1111/1755-0998.70100 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video 17:09 Biodiversity Genomics Europe in Numbers: Sampling, Processing, and Community Lessons Learned What does it take to move from a biological specimen to a sequence-ready sample? In this video, Rita Monteiro presents the work of BGE WP5, which helped connect sample providers, specimens, sequencing centres, and metadata workflows across the community. Alongside a summary of activities and progress, the presentation also reflects on community engagement with the ERGA Manifest and the lessons learned along the way. 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video 04:22 Community-Driven Reference Genomes: Getting to Know Leviellus thorelli In this video, Matjaz Gregoric Leviellus thorelli, one of the species selected for sequencing as part of Biodiversity Genomics Europe. This session focuses on getting to know the species and how reference genome generation can support future research. 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video 24:18 Actions and Plans for Genomes on a Tree (GoaT): Addressing ERGA Feedback (Cibele Sotero-Caio) https://www.erga-biodiversity.eu/post/addressing-erga-community-feedback-actions-and-plans-for-genomes-on-a-tree-goat #erga Genomes on a Tree (GoaT) is a searchable datastore of genome-relevant metadata for eukaryotic species based on aggregated information on completed sequencing efforts (e.g. assembly metrics) and metadata dispersed across specialised databases (e.g. karyotype, genome size, country lists, etc.). GoaT collates information on sequencing intent and progress across more than 40 Earth BioGenome Project affiliates, including several initiatives under the ERGA umbrella (e.g. ATLASea, DToL, ERGA-Pilot, ERGA-BGE, Yggdrasil). GoaT generates summary values at species level by collating all existing observations for a taxon. At higher taxonomic ranks, summaries are inferred from aggregation of observed values across descendant taxa. When species-level data are unavailable, GoaT estimates values based on observations from related taxa sharing a common ancestor. On the GoaT web site, estimated values are visualised through colour-coded, thermometer-style icons, allowing users to identify interpolated data and evaluate the suitability of any estimates for their particular use case according to how far up the phylogenetic tree the underlying estimates originate. These inferred values have proven valuable for production genomics, helping to guide the allocation of sequencing resources, as well as informing expectations about genomic features in poorly characterised taxa. As the GoaT user base continues to expand, the flexible design of the resource does not always align with the expectations or needs of all user groups, particularly non-specialist users. To address this, the GoaT team collaborated with the ERGA communications team to design and disseminate a user survey aimed at: (1) characterising the GoaT user base among ERGA members, (2) identifying key challenges faced by users, and (3) collecting feedback to improve usability and user experience. Survey insights informed the development of a targeted strategy to address identified issues, clarify common misunderstandings, and produce tutorials and support materials. In this talk, I will present the actions taken in response to ERGA community feedback, outline current plans, and demonstrate how users can engage with the GoaT team to contribute and request content as we work to maximise the usability of the resource. Play Video Play Video 03:47 Propomacrus cypriacus - Anna Papadopoulou Learn more about ‪@biodiversitygenomicseurope6700‬ : https://biodiversitygenomics.eu/ Play Video Play Video 28:13 ATLASea - progress on sequencing marine biodiversity (Hugues Roest Crollius) https://www.erga-biodiversity.eu/post/atlasea-progress-on-sequencing-marine-biodiversity The ATLASea program (https://www.atlasea.fr) aims to unlock the potential of marine biodiversity genomes for fundamental research and applications. Funded by the French government for eight years, ATLASea conducts large-scale sampling across the French Exclusive Economic Zone (EEZ) to collect eukaryotic marine specimens and produce 4,500 high-quality reference genomes.

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Structural annotation - So you want to annotate protein-coding genes in your genome? Version 1.0 - August 2023 Top of Page 1. Before you start 2. Do you want to do your own annotation? 3. Evaluate your Annotation 4. Finalise your Annotation Authors : Alice Dennis, Jèssica Gómez, Leanne Haggerty, Lucile Soler, Aureliano Bombarley, Henrik Lantz, Florian Maumus, Hugues Roest Crollius, Fergal Martin, Jean-Marc Aury, Christian deGuttry, Robert Waterhouse, and the ERGA Annotation committee . STEP 1 - Before you start Step 1a: Be sur e the a ssembly is done and you are working with a frozen/stable version! Tabl e 1: Genome assembly evaluation before annotation. Rationale: Low consensus accuracy, incomplete genomes, and contamin ations lead to po or annotation. It is thus essential to evaluate your genome before you start the annotation process. 1. Consensus Accuracy and assembly completeness evaluated (suggestion: Merqury) 2.Gene space complet eness evaluated by: a. Conserved gene space (suggestion: BUSCO ) b. RNA-Seq mappig (suggestion: STA R /Minimap2 ) 3. Organelle/Contamination screening and removal: a. Organelle Genomes( suggestion: Minimap2 ) b. Contaminations (suggestion: BlobTools ) 4. Unc ollapsed duplication for the consensus haploid assembly (suggestion: purge_dups ) 5. Full THE completeness evaluated with the LAI (suggestion: LTR_Retriever ) 6. Does Your genome meet E BP standards ? Step 1b: Is your assembly done? If yes go to Step 1C , if no go to Table 1 . Step 1c: Is the assembly publicly available? Public release is necessary for annotation by Ensembl. If yes go to Step 1d, if no, go to Step 2. Step 1d: Is the public assembly linked to ERGA? If yes, go to Step 1f. If no, go to Step 1e Step 1f: This will make the assembly available for annotation at Ensembl rapid provided that relevant transcriptomic data are also publicly available (ENA). Step 1e : Instructions on how to link your project to ERGA STEP 2 - Do you want to do your own annotation? S tep 2a: Do you want to do your own annotation? If yes, go to Step 2b Step 2b: Gather all available Evidence data: Transcriptomic and protein datasets to support the annotation process. Table 2: Evaluation of your evidence data: the accuracy of the genome annotation process is very sensitive to the amount and quality of your evidence data. 1. RNA-Seq transcriptomic data a. Mapping evaluation (suggestion STAR ). b. Transcript models (suggestion: StringTie ). c. Gene space completeness (suggestion: BUSCO ). 2. Protein d ataset a. Gene space compl eteness (suggestion: BUSCO ). b. Percentage of full protein alignments (suggestion: Spaln ). 3. I soSeq transc riptomic data a. Mapping evaluation (suggestion: Minimap2 ). b. Transcript models (suggestion : StringTie ). c.Gene space completeness (suggestion: BUSCO ). Done? If yes, go to Step 2c . Step 2c : Repeat prediction. ERGA recommends: Repeat Modeler2 , Repeat Masker , Protein Excluder, TEclass , PASTEC , TEdenovo . Done? If yes, go to Step 2d . Step 2d : Ab initio training and prediction. ERGA recommends: AUGUSTUS and Gene Mark-ET/EP/ETP. Step 2e : Gene modelling. ERGA recommends: TSEBRA (BRAKER based predictions), Evidence Modeler , and MAKER . Done? For an evaluation of your evidence data go back to Table 2 . Once done, you are ready for the final quality and contamination check and you can go to Step 3a . STEP 3 - Evaluate your annotation Step 3a : Evaluate your annotation. There is no temporal order for the following suggestions: Step 3b : MAKER eAED scores. Step 3c : Gene family analysis. Step 3d : Genome visualization: 1. IGV ; 2. A pollo (manual curation); 3. EasyGB (JBrowser for a simple dataset). Step 3e : Generate basic gene model summary statistics and compare with related species. Step 3f : BUSCO , visual inspection in browser in context with evidence. Step 3g : Use mapped reads to estimate: 1. How many apparently transcribed regions don't have annotation?; 2. How many genes or exons are supported by read data? Step 3h : Compare gene content to related species with similar annotation approach. Happy with the metrics assessment of each of the parameters for which the annotation has been evaluated? Remember that some of them may depend on the phyla. This is your DIY annotation v1. Again, this is a stopping place. Do not go forward until this is complete. If you are happy with the metric assessment, you can move to Step 4 . STEP 4 - Finalise your annnotation Step 4a : Create proper file formats (ENA GFF3 format r ecommendations). Consider to change the Identifiers produced by the different gene annotation tools (e.g., gene-1) for a more meaningful Identifier (SpeciesCode+AssemblyVersion+Chr/Scf/Ctg-XXX+G+YYYYYY). Step 4b: Provide this annotation to Ensembl as a second track (via GFF3 submission to ENA) and go back to Step 1f. 1. Before you start 2. Do you want to do your own annotation? 3. Evaluate your Annotation 4. Finalise your Annotation