Faculty of Science

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Long-Read Microbial Genomics
Provider: Faculty of Science

Activity no.: 5802-27-00-00	There are 35 available seats
	Enrollment deadline: 01/05/2027

Place	Department of Food Science
Date and time	17.05.2027, at: 00:00 - 28.05.2027, at: 16:00
Regular seats	35
Lecturers	Lukasz Krych
ECTS credits	3.00

Contact person	Lukasz Krych E-mail address: krych@food.ku.dk

Enrolment Handling/Course Organiser	PhD Administration SCIENCE E-mail address: phdcourses@science.ku.dk

Enrolment guidelines This is a toolbox course where 80% of the seats are reserved for PhD students enrolled at the Faculty of SCIENCE at UCPH and 20% of the seats are reserved for PhD students from other Danish Universities/faculties (except CBS). Seats will be allocated on a first-come, first-served basis and according to the applicable rules. Anyone can apply for the course, but if you are not a PhD student at a Danish university (except CBS), you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Aim and Content Long-read sequencing using Oxford Nanopore Technologies (ONT) has rapidly transformed microbial genomics by enabling complete genome reconstruction, including plasmids, and improved taxonomic classification. This intensive one-week course provides hands-on training in nanopore-based analysis of both single bacterial isolates and mixed microbial communities (metagenomics). Participants will gain practical experience in DNA library preparation using both Native and Rapid ONT protocols, followed by sequencing and downstream analysis of long-read data. The course emphasizes working directly with raw nanopore data (pod5/fastq) and applying state-of-the-art tools for genome assembly, strain resolution, and taxonomic classification. For isolate genomics, participants will assemble complete bacterial genomes and plasmids using tools such as Hybracter and recover high-quality genomes with MMLong2. Taxonomic classification will be performed using GTDB-based approaches. For metagenomic samples, participants will learn to classify microbial communities using Metabuli. The course is designed for PhD students and industry professionals and combines lectures, laboratory work, and computational exercises. Learning outcomes • Assess DNA quality and suitability for long-read sequencing • Prepare sequencing libraries using ONT Native and Rapid protocols • Operate nanopore sequencing platforms and handle raw data (pod5/fastq) • Perform quality control and preprocessing of long-read sequencing data • Assemble complete bacterial genomes and plasmids using Hybracter • Recover high-quality genomes using MMLong2 • Perform taxonomic classification of complete and near complete genomes using GTDB-based tools • Calculate Average Nucleotide Identity (ANI) and Digital DNA-DNA Hybridization (dDDH) • Analyze metagenomic datasets using Metabuli Knowledge: • Principles of long-read sequencing technologies (e.g., Oxford Nanopore) • Concepts of microbial genome structure, including plasmids • Fundamentals of genome assembly and strain resolution • Theoretical basis of taxonomic classification using genomic data • Concepts behind Average Nucleotide Identity (ANI) and dDDH • Differences between isolate genomics and metagenomics approaches • Strengths and limitations of long-read sequencing compared to other methods Skills: • Perform DNA quality assessment for long-read sequencing • Prepare sequencing libraries using ONT Native and Rapid protocols • Operate nanopore sequencing instruments and generate sequencing data • Process and manage raw sequencing data (pod5/fastq formats) • Conduct quality control and preprocessing of long-read datasets • Assemble bacterial genomes and plasmids using bioinformatics tools • Perform taxonomic classification using genome-based methods • Calculate genomic similarity metrics (ANI and dDDH) Competences: Upon completion, participants will be competent to: • Integrate laboratory techniques with computational bioinformatics analyses • Critically evaluate sequencing data quality and analysis outputs • Select appropriate tools and methods for genome assembly and classification • Interpret genomic and metagenomic results in a biological context • Solve practical challenges in microbial genomics data analysis • Work independently with sequencing platforms and bioinformatics pipelines Target Group The course is primarily aimed at PhD students and early-career researchers working in microbial genomics, bacterial genetics, metagenomics, and DNA sequencing technologies. It is also highly relevant for laboratory technicians and professionals from industry and private companies who are involved in sequencing-based workflows, microbiome analysis, or bioinformatics data analysis. Recommended Academic Qualifications Participants should have a background in microbiology, molecular biology, biotechnology, bioinformatics, food science, or environmental science. Basic familiarity with DNA sequencing technologies and microbial genomics is recommended. Research Area The course is relevant to research within microbial genomics, microbiology, molecular biology, biotechnology, bioinformatics, food science, and environmental science. It is particularly suited for research focusing on long-read sequencing, genome assembly, metagenomic analysis, microbial ecology, and genomics-driven approaches in both academic and industrial settings. Teaching and Learning Methods The course combines theoretical instruction and practical training to provide participants with both conceptual understanding and hands-on experience. Instruction includes: • Lectures (22 hours): Introduction to long-read sequencing technologies (Oxford Nanopore), microbial genomics, genome assembly, and taxonomic classification approaches. • Laboratory Sessions (7.5 hours): Hands-on training in DNA quality assessment, library preparation, and operation of nanopore sequencing platforms. • Computational Exercises (13 hours): Guided analysis of long-read sequencing data, including preprocessing, genome assembly, taxonomic classification, and metagenomic analysis using relevant bioinformatics tools. • Course Preparation (20 hours): Pre-reading and familiarization with sequencing technologies and basic bioinformatics concepts. • Theoretical Exercises (20 hours): Independent work where participants analyze provided datasets and prepare a short report describing workflows, results, and interpretation. The format ensures the workload equivalent to 3 ECTS (82.5 hours total). Type of Assessment • Assemble a complete bacterial genome from long-read sequencing data using relevant bioinformatics tools. • Perform gene prediction and functional annotation of the assembled genome. • Document the analysis workflow, including key steps, tools, and parameters used. • Prepare a short-written report that presents a walkthrough of the analysis pipeline. • Interpret and discuss the results, including raw data quality, assembly outcomes, and biological relevance. • Assessment will be conducted on a pass/fail basis, based on the quality and completeness of the submitted report, as well as active participation during the course. Course coordinator Associate professor Lukasz Krych Guest Lecturers Axel Soto Serrano - axel.soto@food.ku.dk - Postdoc at University of Copenhagen, Dpt of Food Science Topics: Genome assembly with Hybracter, MAGs recostruction with MMLong2. Bacterial classification with GTDB-based tools. * Eoghan Thomas Reilly - eoghan@food.ku.dk - Bioinformatician at University of Copenhagen, Dpt. of Food Science Topics: Metagenomic Classification with metabuli, Introduction to Average Nucleotide Identity (ANI) and Digital DNA-DNA Hybridization (dDDH) Expected frequency The course will be offered annually. The course is develop on request of students attendig other corse utilising the same technology but different applicartion. Course location** The course will be offered annually. It has been developed in response to requests from students attending other courses that utilize the same technology but focus on different applications. Requirements for signing up Seats for PhD students from Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules of the PhD School. Applications from other participants (including international PhD students, laboratory technicians, and industry specialists) will be considered after the registration deadline. Course fee and participant fee PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types. In addition to the course fee, there might also be a participant fee. If the course has a participant fee, this will apply to all participants regardless of participant type - and in addition to the course fee. Course fee • Participant fee: DKK 1.000 (All participants and in addition to course fee) to over food (lunch, and snacks), coffee etc. • PhD student enrolled at SCIENCE: DKK 0 • PhD student from Danish PhD school Open market: DKK 0 • PhD student from Danish PhD school not Open market: DKK 3.600 • PhD student from foreign university: DKK 3.600 • Master's student from Danish university: DKK 0 • Master's student from foreign university: DKK 3.600 • Non-PhD student employed at a university (e.g., postdocs): DKK 3.600 • Non-PhD student not employed at a university (e.g., from a private company): DKK 10.080 Participants will receive an email with a link and instructions for payment after completing the course Cancellation policy * Cancellations made up to two weeks before the course starts are free of charge. * Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000 * Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000 * No-show will result in a fee of DKK 5.000 * Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000

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