Eukaryotic Genome Sequence Assembly and Annotation
Licence: Creative Commons Attribution 4.0 International
Keywords: Data management, Sequence assembly, Genomics, FAIR
Contributors: Robert Waterhouse, Anthony Bretaudeau, Valeria Di Cola, Anne-Françoise Adam-Blondon, Patricia Palagi
Scientific topics: Genomics, Data management, Biodiversity, Sequence assembly, Sequence analysis, FAIR data
Status: Active
Target audience: Bioinformatician, Biologist, Data Scientist, genomics researchers
Learning objectives:
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 torsten schwede & thierry sengstag group -
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 Data management CONVERGE Data Stewardship Wizard Data management plan
Introduction to genome sequencing
•• Intermediate 4 materials-
e-learning
Data submission using ENA upload Tool
• BeginnerEcology Biodiversity Ecology biodiversity -
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
• BeginnerMetagenomics Sequence assembly Microbial ecology Microbiome 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 Comparative genomics
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

Switzerland