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Welcome to the SequAna_course2024 wiki!

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.	Ms. Verena Ras	Bioinformatics Program Manager, University of Cape Town, South Africa	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/mini-practice
	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
	11:15 - 11:45	Working with Docker images	Ms. Yulia Iakovleva	Software engineer, BioNTech SE, Germany	Practical
	11:45 - 12:30	lunch
	12:30 - 15:00	Workflow management with Nextflow	Mr. Christopher Hakkaart	Developer Advocate at Seqera	lecture/Practical
	15:00 - 15:30	Break
	15:30 - 18:00	Introduction to nf-core	Mr. Christopher Hakkaart	Developer Advocate at Seqera	lecture/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
	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
	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	Gene prediction concept	Dr. Swati Sinha	Senior Bioinformatician, Ensembl Genome Annotation Project, EMBL-EBI, UK	lecture
	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. Hassan Tarabai	Bioinformatician, South Bohemia University, Czechia	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
	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
	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
	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
	11:45 - 12:30	lunch
	12:30 - 14:45	Orthology Prediction and Phylogenetic Analysis	Dr. Abdoallah Sharaf	SequAna Bioinformatician	lecture/mini-practice
	14:45 - 15:00	Break
	15:00 - 16:00	Troubleshooting session with all the participants.	SequAna's Instructors
	16:00 - 16:30	Closing.	Prof. Christian Voolstra	SequAna Director