biodiversity

Tutorials covering biodiversity

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Assembly

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of the mitochondrial genome from PacBio HiFi reads
biodiversity
Chloroplast genome assembly
plants nanopore jbrowse1 biodiversity
Decontamination of a genome assembly
biodiversity
ERGA post-assembly QC
plants animals genome assembly QC biodiversity
Genome Assembly Quality Control
assembly quality control biodiversity
Genome assembly using PacBio data
assembly pacbio biodiversity
Large genome assembly and polishing
assembly polishing nanopore plants biodiversity
Unicycler Assembly
prokaryote microgalaxy biodiversity
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19 biodiversity
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP biodiversity
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
pacbio eukaryote VGP biodiversity

Climate

Lesson Slides Hands-on Recordings Input dataset Workflows
Getting your hands-on earth data
earth-system ocean land atmosphere biodiversity

Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Audio data annotation with NEAL (Nature + Energy Audio labeler)
ecology biodiversity sound media annotation
Biodiversity data exploration
taxonomic data data quality biodiversity
Champs blocs indicators
ecosystem EBV class EBV dataset EBV workflow marine ecosystems biodiversity
Cleaning GBIF data for the use in Ecology
gbif data management data cleaning biodiversity
Cleaning GBIF data using OpenRefine
biodiversity data cleaning
Compute and analyze biodiversity metrics with PAMPA toolsuite
species population EBV class community composition EBV class EBV dataset EBV workflow modeling biodiversity
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
metadata EML FAIR data paper biodiversity
Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
metadata EML ecology biodiversity FAIR data paper
Data submission using ENA upload Tool
biodiversity
Ecoregionalization workflow tutorial
ecology taxonomic data EBV workflow modeling gbif ocean earth-system interactive-tools biodiversity
Life Traits Ecoregionalization workflow
biodiversity ecoregions life traits
Marine Omics identifying biosynthetic gene clusters
earth-system ocean marine omics biodiversity
Metabarcoding/eDNA through Obitools
genetic composition EBV class community composition EBV class EBV dataset EBV workflow eDNA metabarcoding biodiversity
Obis marine indicators
earth-system ocean marine omics biodiversity
Phylodiversity analysis quick tutorial
ecology taxonomic data phylodiversity biodiversity
Preparing genomic data for phylogeny reconstruction
phylogeny data handling functional annotation biodiversity
QGIS Web Feature Services
earth-system GIS Geographical Information System WFS spatial data maps OGC biodiversity
RAD-Seq Reference-based data analysis
RAD-seq genetic composition EBV class species population EBV class EBV dataset EBV workflow biodiversity
RAD-Seq de-novo data analysis
RAD-seq genetic composition EBV class species populations EBV class EBV dataset EBV workflow biodiversity
RAD-Seq to construct genetic maps
RAD-seq genetic composition EBV class EBV dataset EBV workflowz biodiversity
Regional GAM
species populations EBV class species traits EBV class EBV dataset EBV workflow biodiversity
Sentinel 2 biodiversity
Remote sensing biodiversity
Species distribution modeling
interactive-tools modeling gbif species populations EBV class biodiversity
Taxonomic Analysis of eDNA
biodiversity metabarcoding
Object detection with YOLO
object-detection deep-learning ecology biodiversity marine

Genome Annotation

Lesson Slides Hands-on Recordings Input dataset Workflows
Comparison of two annotation tools - Helixer and Braker3
eukaryota Braker3 Helixer jbrowse1 biodiversity
Genome annotation with Braker3
eukaryota Braker3 jbrowse1 biodiversity
Genome annotation with Helixer
eukaryota helixer jbrowse1 biodiversity
Masking repeats with RepeatMasker
eukaryote biodiversity
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy biodiversity
Genome annotation with Funannotate
gmod eukaryote jbrowse1 biodiversity
Functional annotation of protein sequences
eukaryote biodiversity
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity

Contributors

This material was contributed to by:

Anton Nekrutenko avatar Anton Nekrutenkoorcid logoAnkerl Yassine avatar Ankerl Yassineorcid logoJonathan Kreplak avatar Jonathan KreplakElisa Michon avatar Elisa Michonorcid logoLaura Leroi avatar Laura Leroiorcid logoNate Coraor avatar Nate CoraorSimon Benateau avatar Simon Benateauorcid logoWendi Bacon avatar Wendi BaconFabian Recktenwald avatar Fabian RecktenwaldMarius van den Beek avatar Marius van den BeekJean Le Cras avatar Jean Le Crasorcid logoWolfgang Maier avatar Wolfgang MaierTanguy Genthon avatar Tanguy GenthonClara Urfer avatar Clara UrferFrédéric Boyer avatar Frédéric Boyerorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoSolenne Correard avatar Solenne Correardorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoRomane LIBOUBAN avatar Romane LIBOUBANMiguel Roncoroni avatar Miguel RoncoroniElouan Le Mestric avatar Elouan Le Mestricorcid logoErwan Corre avatar Erwan CorreLaura Russell avatar Laura Russellorcid logoMateo Boudet avatar Mateo Boudetorcid logoStéphanie Robin avatar Stéphanie RobinOlivier Norvez avatar Olivier NorvezDominique Pelletier avatar Dominique PelletierMarcella Sozzoni avatar Marcella Sozzoniorcid logoTom Brown avatar Tom BrownJean-Baptiste Mihoub avatar Jean-Baptiste MihoubHaswane Chei avatar Haswane CheiNathan Dunn avatar Nathan Dunnorcid logoAnna Syme avatar Anna SymeSimon Bray avatar Simon Brayorcid logoDaniela Schneider avatar Daniela SchneiderMohammad Joudy avatar Mohammad JoudyJohn Beliveau avatar John BeliveauGildas Le Corguillé avatar Gildas Le CorguilléSophie Pamerlon avatar Sophie Pamerlonorcid logoYvan Le Bras avatar Yvan Le BrasBrandon Pickett avatar Brandon Pickettorcid logoNicola Soranzo avatar Nicola SoranzoGiulio Formenti avatar Giulio Formentiorcid logoColine Royaux avatar Coline RoyauxNiall Beard avatar Niall Beardorcid logoLinelle Abueg avatar Linelle Abuegorcid logoAlex Ostrovsky avatar Alex OstrovskyVerena Moosmann avatar Verena Moosmannorcid logoAlexandre Cormier avatar Alexandre CormierMarie Josse avatar Marie JosseJasper Ouwerkerk avatar Jasper OuwerkerkWilliam Durand avatar William Durandorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoTeresa Müller avatar Teresa MüllerNajat Amoukou avatar Najat Amoukouorcid logoBrigida Gallone avatar Brigida Galloneorcid logoMartin Čech avatar Martin ČechEnis Afgan avatar Enis Afganorcid logoSimon Gladman avatar Simon Gladmanorcid logoDeepti Varshney avatar Deepti VarshneyArthur Barreau avatar Arthur Barreauorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoDelphine Lariviere avatar Delphine LarivierePerrine Jégousse avatar Perrine Jégousseorcid logoCristóbal Gallardo avatar Cristóbal GallardoEric Coissac avatar Eric Coissac

Funding

These individuals or organisations provided funding support for the development of this resource

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MNHN
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PNDB
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GBIF
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FNSO
This project (AAPFNSO2019OpenMetaPaper-14026) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.
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Australian BioCommons
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The University of Melbourne
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Fair-Ease
FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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ELIXIR Europe
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Antarctic and Southern Ocean Coalition
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IFB
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Melbourne Bioinformatics
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.