Within the Biodiversity Genomics Europe project, the "High Mountain Systems - Arthropods" case study was designed to evaluate how arthropod communities change along altitudinal gradients in seven selected mountain systems across different countries in Europe, establishing baseline sampling in mountain ranges to track biodiversity shifts associated with climate change. This SOP describes the sampling design and fieldwork methodology for retrieving arthropod bulk samples for metabarcoding analyses. ...
Creators: Laura Najera Cortazar, Sonia Ferreira, Vanessa Mata, Pedro Beja
Submitter: Laura Najera Cortazar
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This is a project specific guide for the Bioiversity Genomics Europe (BGE project use of WorkflowHub.
External LinkThe BioDT project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:
- To give visibility to the workflows created by the project and by the different networks and communities within the project
- To give visibility to the workflows used by project that were created
- To share workflows across the project, within project networks and externally
- To credit and cite the people making the workflows and the networks to which they ...
Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "OBIS marine indicators" .
This workflow allows to compute and visualize marine biodiversity indicators from OBIS data.
Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.5 km2 large Reserve Naturelle Nationale du Bagnas ('Bagnas') in France (3.514360 E, 43.314332 N). The work has been performed in the context of the EU project MAMBO (Modern ...
Type: Jupyter
Creators: W. Daniel Kissling, Wessel Mulder, Jinhu Wang, Yifang Shi
Submitter: W. Daniel Kissling
skim2mito
skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and ...
Galaxy-E (ecology.usegalaxy.eu) workflow to calculate species presence / absence, community metrics and compute generalized linear models to identify effects and significativity of these effects on biodiversity.
Pipelines used by the genomes assembly teams part of the Biodiversity Genomics Europe project
This is a general collection of workflows used by or developed by members of the BGE project.
