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Abdoallah Sharaf edited this page Apr 1, 2024
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© 2024 Abdoallah Sharaf
Day | Time (CET) | Session Title | instructor | Affiliation | Notes |
---|---|---|---|---|---|
DAY I: Thursday 21.03.2024 | 9:00 - 9:15 | Opening | Prof. Christian Voolstra | SequAna Director | lecture |
9:15 - 10:00 | Course instructions | SequAna's Instructors | lecture | ||
10:00 - 10:15 | Break | ||||
10:15 - 11:00 | Design of a genome sequencing experiment | Dr. Abdoallah Sharaf | SequAna Bioinformatician | lecture | |
11:00 - 11:45 | Nanopore Sequencing technologies. | Dr. Nicolai Stoye | Senior Account Manager, Oxford Nanpore | lecture | |
11:45 - 12:30 | lunch | ||||
12:30 - 13:30 | Working on the command line interface (CLI) and using package managers to install programs | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
13:30 - 13:45 | Break | ||||
13:45 - 18:00 | Practice on high molecular weight and library prep strategies. | Ms. Alyssa Bell | SequAna Lab. technician | Practical | |
DAY II: Friday 22.03.2024 | 9:00 - 9:45 | k-mer and ploidy profilling | Dr Kamil S Jaron | Group Leader, Welcome Sanger Institute, UK | lecture/Zoom |
9:45 - 11:15 | Querying genome metadata and sequencing projects using GoaT | Dr. Cibele Sotero-Caio | Genomic Data Curator - Tree of Life Genomics, Welcome Sanger Institute, UK | lecture/mini-practice/Zoom | |
11:15 - 11:45 | Working with Docker images | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
11:45 - 12:30 | lunch | ||||
12:30 - 15:00 | Workflow management with Nextflow | Mr. Christopher Hakkaart | Developer Advocate at Seqera | Zoom/Practical | |
15:00 - 15:30 | Break | ||||
15:30 - 18:00 | Introduction to nf-core | Mr. Christopher Hakkaart | Developer Advocate at Seqera | Zoom/Practical | |
DAY III: Monday 25.03.2024 | 9:00 - 10:45 | Principles of genome assembly | Prof. Jean-François Flot | Group Leader, Université libre de Bruxelles (ULB), Brussels, Belgium | lecture/Zoom |
10:45 - 11:00 | Break | ||||
11:00 - 11:45 | sequencing reads pre-processing and quality control | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
11:45 - 12:30 | lunch | ||||
12:30 - 13:00 | Genome k-mer profiling | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
13:00 - 13:45 | De-novo assembly using Oxford Nanopore sequencing reads | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
13:45 - 14:00 | Break | ||||
14:00 - 15:30 | Genome assembly assessment | Dr. Giulio Formenti | Lead Bioinformatician, Vertebrate Genome Laboratory, Rockefeller University, USA | lecture/mini-practice/Zoom | |
15:30 - 16:00 | Break | ||||
16:00 - 17:00 | Visualizing genome assembly cobionts by running BlobToolKit locally | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
17:00- 18:00 | Assembling organelle genomes | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
Day IV: Tuesday 26.03.2024 | 9:00 - 9:45 | Eukaryotic Genome Annotation | Dr. Swati Sinha | Senior Bioinformatician, Ensembl Genome Annotation Project, EMBL-EBI, UK | lecture/Zoom |
9:45 - 10:00 | Break | ||||
10:00 - 11:45 | Identification and masking of DNA repeats | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
11:45 - 12:30 | lunch | ||||
12:30 - 14:00 | Gene prediction and functional annotation using Funannotate | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
14:00 - 14:45 | Characterization and annotation of DNA repeats | Dr. Shujun Ou | Assistant Professor, Department of Molecular Genetics, Ohio State University, USA | lecture/Zoom | |
14:45 - 15:00 | Break | ||||
15:00 - 16:30 | ENA Standards and Submission | Ms. Maira ihsan | User Support Bioinformatician, EMBL-EBI. UK | lecture/mini-practice/Zoom | |
16:30 - 16:45 | Break | ||||
16:45 - 18:00 | Searching and Downloading Genome Data using NCBI Datasets | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
Day V: Wednesday 27.03.2024 | 9:00 - 9:45 | BUSCO - from QC to gene prediction and phylogenomics | Dr. Robert M. Waterhouse | Group Leader, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland | lecture/mini-practice/Zoom |
9:45 - 10:00 | Break | ||||
10:00 - 11:45 | FastOMA for homology exploration | Dr. Sina Majidian/Dr. Yannis Nevers | Postdoctoral Fellows, Dessimoz’s lab, University of Lausanne | lecture/mini-practice/Zoom | |
11:45 - 12:30 | lunch | ||||
12:30 - 13:30 | Functional Enrichment Analysis | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
13:30 - 14:45 | Comparative Genomic and Phylogenetic Analysis | Dr. Abdoallah Sharaf | SequAna Bioinformatician | Practical | |
15:00 - 16:00 | Troubleshooting session with all the participants. | SequAna's Instructors | |||
16:00 - 16:30 | Closing. | Prof. Christian Voolstra | SequAna Director |