Biodiversity Genomics Europe (BGE)
Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice at multiple scales that translate into building capacity, boosting complementarity among activities in individual countries and establishing mechanisms to democratise participation.
To address this challenge from the European perspective, the BGE consortium, with 33 partners, brings together two newly formed networks:
- BIOSCAN Europe – DNA barcoding
- European Reference Genome Atlas (ERGA) – genome sequencing
The project will tackle three fundamental objectives:
- Establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to tackle the biodiversity crisis using genomic tools.
- Establish and implement large-scale biodiversity genomic data generation pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation and biomonitoring.
- Apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes.
This WorkflowHub space will be used to gather computational workflows develoepd within the BGE consortium.
Web page: https://biodiversitygenomics.eu/
Funding codes:- https://doi.org/10.3030/101059492
- https://gtr.ukri.org/projects?ref=10040409
HORIZON-CL6-2021-BIODIV-01-01 101059492
Related items
Teams: iwc, Vertebrate Genomes Pipelines in Galaxy
Organizations: Bots, European Galaxy Team
Teams: Vertebrate Genomes Pipelines in Galaxy
Organizations: Galaxy
https://orcid.org/0000-0001-6421-3484
Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection, BY-COVID (general), BioDT additional pipelines, BioDT Use Case 4.1.1.1 Biodiversity dynamics, BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats, BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security, BioDT Use Case 4.1.3.1 Invasive species, BioDT Use Case 4.1.3.2 Endangered species, BioDT Use Case 4.1.4.1 Disease outbreaks, BioDT Use Case 4.1.4.2 Pollinators, BioDT Use Case 4.1.1.2 Ecosystem services
Organizations: The University of Manchester
https://orcid.org/0000-0001-9842-9718
Teams: Biodiversity Genomics Europe (general)
Organizations: Naturalis
https://orcid.org/0000-0001-9254-7318
This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.
To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://biodiversitygenomics.eu/
Start date: 1st Sep 2022
End date: 28th Feb 2026
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://galaxyproject.org/projects/vgp/workflows/
Country: Not specified
City: Not specified
Web page: Not specified
Country: Not specified
City: Not specified
Web page: Not specified
SOP for DNA extraction and Illumina amplicon library preparation of soil core samples collected for the Case Study "Characterization of Prokaryotic and Eukaryotic Biodiversity from Soil Samples" withing the scope of BGE (Biodiversity Genomics Europe) project.
Creator: Cátia Chaves
Submitter: Cátia Chaves
DownloadSOP for DNA extraction and Illumina amplicon library preparation of encapsulated water samples collected for the Case Study "Detection of Non-Indigenous Marine Species from Port Water Samples" withing the scope of BGE (Biodiversity Genomics Europe) project.
Creator: Cátia Chaves
Submitter: Cátia Chaves
HiC scaffolding pipeline
Snakemake pipeline for scaffolding of a genome using HiC reads using yahs.
Prerequisites
This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:
snakemake --use-conda --cores N
where N is number of cores to use. There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring the cluster.json file run:
./run_cluster
...
Purge dups
This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:
snakemake --use-conda --cores N
Or configure the cluster.json and run using the ./run_cluster command
HiC contact map generation
Snakemake pipeline for the generation of .pretext and .mcool files for visualisation of HiC contact maps with the softwares PretextView and HiGlass, respectively.
Prerequisites
This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:
snakemake --use-conda
There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring ...
Bactria: BarCode TRee Inference
...
