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:

orcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMartin Čech avatar Martin ČechMohammad Joudy avatar Mohammad JoudyTanguy Genthon avatar Tanguy Genthonorcid logoBérénice Batut avatar Bérénice Batutorcid logoMarie Josse avatar Marie JosseBrandon Pickett avatar Brandon PickettNajat Amoukou avatar Najat AmoukouEnis Afgan avatar Enis Afganorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoLinelle Abueg avatar Linelle AbuegHaswane Chei avatar Haswane Cheiorcid logoCristóbal Gallardo avatar Cristóbal GallardoKevin Payet avatar Kevin PayetNathan Dunn avatar Nathan DunnMiguel Roncoroni avatar Miguel Roncoroniorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoAnkerl Yassine avatar Ankerl YassineFabian Recktenwald avatar Fabian Recktenwaldorcid logoFelicitas Kindel avatar Felicitas KindelNiall Beard avatar Niall BeardOlivier Norvez avatar Olivier NorvezPerrine Jégousse avatar Perrine Jégousseorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoStéphanie Robin avatar Stéphanie RobinJohn Beliveau avatar John BeliveauJean Le Cras avatar Jean Le CrasWilliam Durand avatar William Durandorcid logoColine Royaux avatar Coline Royauxorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoErwan Corre avatar Erwan Correorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoAnna Syme avatar Anna SymeEric Coissac avatar Eric Coissacorcid logoAlex Ostrovsky avatar Alex OstrovskyJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoWendi Bacon avatar Wendi Baconorcid logoAnne Fouilloux avatar Anne FouillouxJean-Baptiste Mihoub avatar Jean-Baptiste MihoubSimon Bray avatar Simon BrayGildas Le Corguillé avatar Gildas Le Corguilléorcid logoRomane LIBOUBAN avatar Romane LIBOUBANElisa Michon avatar Elisa MichonElouan Le Mestric avatar Elouan Le Mestricorcid logoTom Brown avatar Tom BrownClara Urfer avatar Clara Urferorcid logoNate Coraor avatar Nate Coraororcid logoHelena Rasche avatar Helena Rascheorcid logoBrigida Gallone avatar Brigida Galloneorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn Grüningorcid logoSimon Gladman avatar Simon Gladmanorcid logoMateo Boudet avatar Mateo BoudetLaura Russell avatar Laura Russellorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia HiltemannDominique Pelletier avatar Dominique PelletierVerena Moosmann avatar Verena MoosmannSimon Benateau avatar Simon Benateauorcid logoNadine Le Bris avatar Nadine Le Brisorcid logoSolenne Correard avatar Solenne Correardorcid logoTeresa Müller avatar Teresa MüllerArthur Barreau avatar Arthur BarreauFrédéric Boyer avatar Frédéric Boyerorcid logoJonathan Kreplak avatar Jonathan KreplakGiulio Formenti avatar Giulio FormentiMarcella Sozzoni avatar Marcella SozzoniSophie Pamerlon avatar Sophie PamerlonAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLaura Leroi avatar Laura Leroiorcid logoMarius van den Beek avatar Marius van den Beekorcid logoDeepti Varshney avatar Deepti Varshney

Funding

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

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