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

Earth Data Science

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
Object detection with YOLO
object-detection deep-learning ecology biodiversity marine
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

Genome Annotation

Lesson Slides Hands-on Recordings Input dataset Workflows
Masking repeats with RepeatMasker
eukaryote biodiversity
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
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
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2

Imaging

Lesson Slides Hands-on Recordings Input dataset Workflows
AI pipeline for annotating marine species (Project Moorev - Marine)
Marine ecosystems biodiversity AI segmentation YOLO deep learning object detection

Contributors

This material was contributed to by:

Elouan Le Mestric avatar Elouan Le Mestricorcid logoAlex Ostrovsky avatar Alex OstrovskyHaswane Chei avatar Haswane CheiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoCristóbal Gallardo avatar Cristóbal GallardoGiulio Formenti avatar Giulio Formentiorcid logoMarie Josse avatar Marie Josseorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoBrigida Gallone avatar Brigida Galloneorcid logoNadine Le Bris avatar Nadine Le Brisorcid logoLinelle Abueg avatar Linelle Abuegorcid logoColine Royaux avatar Coline Royauxorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoNate Coraor avatar Nate CoraorJean-Baptiste Mihoub avatar Jean-Baptiste MihoubVerena Moosmann avatar Verena Moosmannorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoStéphanie Robin avatar Stéphanie RobinFabian Recktenwald avatar Fabian RecktenwaldSophie Pamerlon avatar Sophie PamerlonJean Le Cras avatar Jean Le CrasSimon Bray avatar Simon Brayorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMarius van den Beek avatar Marius van den BeekElisa Michon avatar Elisa Michonorcid logoSolenne Correard avatar Solenne CorreardWilliam Durand avatar William DurandGildas Le Corguillé avatar Gildas Le CorguilléPerrine Jégousse avatar Perrine JégousseNiall Beard avatar Niall Beardorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoSaskia Hiltemann avatar Saskia HiltemannMiguel Roncoroni avatar Miguel Roncoroniorcid logoGlinez Thibaud avatar Glinez ThibaudSimon Benateau avatar Simon BenateauFrédéric Boyer avatar Frédéric Boyerorcid logoJonathan Kreplak avatar Jonathan KreplakEric Coissac avatar Eric Coissacorcid logoDelphine Lariviere avatar Delphine LariviereClara Urfer avatar Clara UrferMohammad Joudy avatar Mohammad Joudyorcid logoMartin Čech avatar Martin ČechLaura Russell avatar Laura RussellOlivier Norvez avatar Olivier NorvezBrandon Pickett avatar Brandon PickettDominique Pelletier avatar Dominique Pelletierorcid logoBérénice Batut avatar Bérénice Batutorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoLaura Leroi avatar Laura Leroiorcid logoAnne Fouilloux avatar Anne FouillouxArthur Barreau avatar Arthur Barreauorcid logoTeresa Müller avatar Teresa MüllerJohn Beliveau avatar John BeliveauEnis Afgan avatar Enis AfganNathan Dunn avatar Nathan Dunnorcid logoAnkerl Yassine avatar Ankerl YassineJasper Ouwerkerk avatar Jasper OuwerkerkMarcella Sozzoni avatar Marcella Sozzoniorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoMateo Boudet avatar Mateo Boudetorcid logoDaniela Schneider avatar Daniela SchneiderNajat Amoukou avatar Najat Amoukouorcid logoTom Brown avatar Tom Brownorcid logoHelena Rasche avatar Helena Rascheorcid logoAnna Syme avatar Anna Symeorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoWendi Bacon avatar Wendi Baconorcid logoSimon Gladman avatar Simon Gladmanorcid logoErwan Corre avatar Erwan CorreKevin Payet avatar Kevin Payetorcid logoAnthony Bretaudeau avatar Anthony BretaudeauTanguy Genthon avatar Tanguy Genthon

Funding

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

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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.
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MOOREV
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ISYEB
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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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PNDB
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SU
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Melbourne Bioinformatics
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ELIXIR Europe
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Antarctic and Southern Ocean Coalition
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The University of Melbourne
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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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IFB
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MNHN
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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.