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
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
Ecoregionalization workflow tutorial
ecology taxonomic data EBV workflow modeling gbif ocean earth-system interactive-tools biodiversity
Life Traits Ecoregionalization workflow
biodiversity
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
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

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