biodiversity

Tutorials covering biodiversity

Material

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

Assembly

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

Earth Data science

Lesson Slides Hands-on Recordings Input dataset Workflows
Getting your hands-on earth data

Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Object detection with YOLO
Audio data annotation with NEAL (Nature + Energy Audio labeler)
Biodiversity data exploration
Champs blocs indicators
Cleaning GBIF data for the use in Ecology
Cleaning GBIF data using OpenRefine
Compute and analyze biodiversity metrics with PAMPA toolsuite
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
Data submission using ENA upload Tool
Ecoregionalization workflow tutorial
Life Traits Ecoregionalization workflow
Marine Omics identifying biosynthetic gene clusters
Metabarcoding/eDNA through Obitools
Obis marine indicators
Phylodiversity analysis quick tutorial
Preparing genomic data for phylogeny reconstruction
QGIS Web Feature Services
RAD-Seq Reference-based data analysis
RAD-Seq de-novo data analysis
RAD-Seq to construct genetic maps
Regional GAM
Sentinel 2 biodiversity
Species distribution modeling
Taxonomic Analysis of eDNA

Genome Annotation

Lesson Slides Hands-on Recordings Input dataset Workflows
Masking repeats with RepeatMasker
Comparative gene analysis in unannotated genomes
Genome annotation with Funannotate
Functional annotation of protein sequences
Refining Genome Annotations with Apollo (eukaryotes)
Comparison of two annotation tools - Helixer and Braker3
Genome annotation with Braker3
Genome annotation with Helixer
Refining Genome Annotations with Apollo (prokaryotes)

Imaging

Lesson Slides Hands-on Recordings Input dataset Workflows
AI pipeline for annotating marine species (Project Moorev - Marine)

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