Switzerland
Eukaryotic Genome Sequence Assembly and Annotation
A learning path set for Eukaryotic Genome Sequence Assembly and Annotation data management with 3 domains : FAIR essentials, genome assembly, and genome annotation.
Licence: Creative Commons Attribution 4.0 International
Keywords: Data management, Sequence assembly, Genomics, FAIR
Contributors: Robert Waterhouse, Anthony Bretaudeau
Scientific topics: Genomics, Data management, Biodiversity, Sequence assembly, Sequence analysis, FAIR data
Status: Active
Target audience: Bioinformatician, Biologist, Data Scientist, genomics researchers
Learning objectives:
At the end of the learning path, researchers or data managers specialized in biodiversity genomics are able to :
- retrieve metadata for the biological materials of their interest
- retrieve unique identifiers for their samples from BioSamples
- retrieve metadata on omics experiments
- publish metadata on omics experiments in the recommended databases
- use tools to version their metadata curation before publication
- submit the raw data and the annotated genomes to ENA, the samples to BioSamples with the correct metadata
- analyze the data of the genome in reproducible way and manage the data in a FAIR way
People should be able to do genome assembly by themself (starting with raw data), and do the functional annotation of the genome that they obtain.
Data Management: Basics of the genome sequencing
• beginner 12 materials-
e-learning
A short introduction to Galaxy
• beginnerIntroduction to Galaxy Analyses español -
e-learning
Galaxy Basics for genomics
• beginnerIntroduction to Galaxy Analyses -
e-learning
An Introduction to Genome Assembly
• beginnerSequence assembly Assembly -
slides
An introduction to scRNA-seq data analysis
•• intermediateTranscriptomics Single Cell -
NGS - Quality Control, Alignment, Visualisation
• beginnertraining genes and genomes next generation sequencing environmental science medicine and health -
e-learning
Name tags for following complex histories
• beginnerUsing Galaxy and Managing your Data -
Introduction to bulk RNA-Seq: From Quality Control to Pathway Analysis
• beginnerfunctional genomics genes and genomes next generation sequencing transcriptomics training -
e-learning
Pre-processing of 10X Single-Cell RNA Datasets
• beginnerTranscriptomics 10x Single Cell -
e-learning
Clustering 3K PBMCs with Scanpy
• beginnerTranscriptomics 10x Single Cell -
Introduction to FAIR Research Data Management & Data Management Plan
• beginnertraining reproducibility data management data security open data mark ibberson group -
Recorded webinar
Principles of research data management
Data management
-
lessons, e-learning
Introduction to Data Management Practices - Data Management Plans
• beginnerData management FAIR data Open science CONVERGE Data Stewardship Wizard Data management plan
Introduction to genome sequencing
•• intermediate 4 materials-
e-learning
Data submission using ENA upload Tool
• beginnerEcology -
Submitting, Finding and Downloading Raw Sequencing Data with ENA
• beginnerFAIR data Metadata Data submission -
e-learning
BioSamples: Quick tour
Data curation and archival Data management Metadata Reference samples Biological samples
-
Recorded webinar
BioSamples: a FAIR sample metadata archive
Data management
Eukaryotic Genome Assembly
••• advanced 23 materials-
e-learning
Genome Assembly Quality Control
•• intermediateSequence assembly Biodiversity Data quality management Assembly assembly biodiversity quality control -
Galaxy Introduction for Life Scientists
• beginnerbasic research experimental biology interoperability next generation sequencing reproducibility training michael stadler group -
e-learning
A short introduction to Galaxy
• beginnerIntroduction to Galaxy Analyses español -
e-learning
Galaxy Basics for genomics
• beginnerIntroduction to Galaxy Analyses -
NGS - Quality Control, Alignment, Visualisation
• beginnertraining genes and genomes next generation sequencing environmental science medicine and health -
slides
Genome assembly and assembly QC - Introduction short version
• beginnerSequence assembly Assembly -
slides
An introduction to get started in genome assembly and annotation
• beginnerSequence assembly Assembly -
e-learning
Assembly of metagenomic sequencing data
• beginnerSequence assembly Metagenomics Assembly assembly metagenomics microgalaxy -
e-learning
Assembly of the mitochondrial genome from PacBio HiFi reads
• beginnerSequence assembly Genomics Biodiversity Mitochondria Assembly biodiversity -
e-learning
De Bruijn Graph Assembly
• beginnerSequence assembly Assembly -
e-learning
Decontamination of a genome assembly
• beginnerSequence assembly Genomics Biodiversity Assembly biodiversity -
slides
Deeper look into Genome Assembly algorithms
•• intermediateSequence assembly Assembly -
e-learning
ERGA post-assembly QC
• beginnerSequence assembly Genomics Biodiversity Assembly QC animals assembly biodiversity genome plants -
Genome Sequencing (Bioinformatics II)
life-sciences computer-science health-informatics algorithms
-
e-learning
Genome assembly using PacBio data
•• intermediateSequence assembly Genomics Biodiversity Assembly assembly biodiversity pacbio -
e-learning
Large genome assembly and polishing
• beginnerSequence assembly Genomics Biodiversity Assembly assembly biodiversity nanopore plants polishing -
e-learning
Making sense of a newly assembled genome
• beginnerSequence assembly Genomics Microbiology Assembly gmod jbrowse1 microgalaxy prokaryote -
e-learning
Unicycler Assembly
• beginnerSequence assembly Genomics Microbiology Assembly biodiversity microgalaxy prokaryote -
e-learning
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
•• intermediateSequence assembly Assembly biodiversity covid19 -
e-learning
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
•• intermediateSequence assembly Chromosome conformation capture Assembly VGP biodiversity eukaryote pacbio -
e-learning
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
•• intermediateSequence assembly Genomics Biodiversity Assembly VGP biodiversity eukaryote pacbio -
Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions
• beginnerbiodiversity non model organisms evolution and phylogeny genes and genomes comparative genomics evolutionary biology training marc robinson-rechavi group robert waterhouse group christophe dessimoz group -
Tutorial, Slides, Scripts
Genome assembly, annotation and comparative genomics - EBP-Nor workshop 2024
Bioinformatics Genomics Comparative genomics Assembly Annotation
Eukaryotic Genome Annotation
••• advanced 11 materials-
slides
Introduction to Genome Annotation
•• intermediateGenomics Genome Annotation -
e-learning
Masking repeats with RepeatMasker
• beginnerGenomics Sequence composition, complexity and repeats Genome Annotation biodiversity eukaryote -
e-learning
Genome annotation with Funannotate
•• intermediateGenomics Gene and protein families Genome Annotation biodiversity eukaryote gmod jbrowse1 -
e-learning
Long non-coding RNAs (lncRNAs) annotation with FEELnc
•• intermediateGenomics Genome Annotation eukaryote -
e-learning
Refining Genome Annotations with Apollo (eukaryotes)
•• intermediateGenomics Genome Annotation apollo2 biodiversity cyoa eukaryote gmod jbrowse1 -
e-learning
Comparison of two annotation tools - Helixer and Braker3
•• intermediateGenomics Sequence assembly Braker3 Genome Annotation Helixer biodiversity eukaryota jbrowse1 -
e-learning
Genome annotation with Braker3
•• intermediateGenomics Sequence assembly Biodiversity Zoology Plant biology Braker3 Genome Annotation biodiversity eukaryota jbrowse1 -
e-learning
Genome annotation with Helixer
•• intermediateGenomics Biodiversity Zoology Plant biology Genome Annotation biodiversity eukaryota helixer jbrowse1 -
e-learning
Genome annotation with Maker (short)
•• intermediateGenomics Genome Annotation eukaryote gmod jbrowse1 maker -
e-learning
Genome annotation with Maker
••• advancedGenomics Genome Annotation eukaryote gmod jbrowse1 maker -
Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions
• beginnerbiodiversity non model organisms evolution and phylogeny genes and genomes comparative genomics evolutionary biology training marc robinson-rechavi group robert waterhouse group christophe dessimoz group
Activity log
