Biodiversity Genomics Europe (general)
OverviewThis 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)
SEEK ID: https://workflowhub.eu/projects/202
Funding codes:- https://doi.org/10.3030/101059492
Public web page: https://biodiversitygenomics.eu/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team start date: 1st Sep 2022
Team end date: 28th Feb 2026
Related items
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
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 ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
Web page: https://biodiversitygenomics.eu/
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
Library curation BOLD
This repository contains scripts and synonymy data for pipelining the automated curation of BOLD data dumps in BCDM TSV ...
Type: Snakemake
Creators: Rutger Vos, Fabian Deister, Ben Price, Special thanks to Sujeevan Ratnasingham and the team at CBG for the creation of the BCDM data exchange format that this pipeline operates on
Submitter: Rutger Vos
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
...
eDNA Protocols for BGE (Biodiversity Genomics Europe) Work package 6, task 6.2
Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.
Development versions of these pipelines can be found in the ERGA github and any questions or queries can be raised on the ERGA Discussions Channel
Want to find out more about the work done by ERGA? Become a member ...
This is a general collection of workflows used by or developed by members of the BGE project.
