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DESCRIPTION:Educators:\nNils Kleinbölting (BiGi)\, Daniel Wibberg (CAU)\, 
 Tobias Busche\, Christian Rückert\, Levin Joe Klages (Omics CF NGS and Ce
 BiTec Technology Platform\, Bielefeld University)\n\nDate:\n30 June - 2 Ju
 ly 2026\n\nLocation:\nBielefeld University\n\nContent:\nThe aim of this wo
 rkshop is to familiarize participants with Oxford Nanopore sequencing tech
 nologies\, its applications\, and the best practice bioinformatics workflo
 w. Participants will gain insights into how this technology facilitates th
 e assembly of prokaryotic genomes and metagenomes\, focusing on establishi
 ng finalized genome sequences and MAGs.\n\nThe workshop will begin with an
  introduction to Nanopore sequencing\, covering its principles and differe
 nces from other sequencing methods. We will discuss the evolution of Long-
 Read technology and its current role in the sequencing landscape. Particip
 ants will also explore various applications\, including genome assembly\, 
 real-time sequencing and transcriptomics\, illustrated by case studies hig
 hlighting its effectiveness in research and clinical settings. A central c
 omponent of the first workshop day is a practical part in which a sequenci
 ng library is first prepared and then used for real-time sequencing.\n\nOn
  the first half of the second day\, students will start getting familiar w
 ith the Linux operating system and receive an introduction to the command 
 line\, with a focus on file and directory management. No prior bioinformat
 ics knowledge is required.\n\nOn the second half of the second day and on 
 the third day\, bioinformatics workflow associated will be outlined\, cove
 ring the standard processes from raw data acquisition to final genome asse
 mbly. Participants will learn about key tools such as Dorado\, Minimap2\, 
 and (meta)Flye\, as well as the advantages and pitfalls of Long-Read seque
 ncing\, including long read lengths and potential error rates.\n\nThe hand
 s-on component will guide participants through a typical workflow\, starti
 ng with basecalling\, data preprocessing and quality control in the de.NBI
  cloud environment. They will practice sequence alignment and genome assem
 bly\, followed by basic genome annotation techniques and a few insights in
 to metagenomics with ONT.\n\nLearning goals:\nThis workshop aims to teach 
 basic skills and best practices to researchers working with Long-Read data
 . The full course will include all necessary steps from an introduction to
  Nanopore sequencing (1)\, raw sequencing data to finalized genomes and MA
 Gs (2) with a de novo assembly and (3) with re-sequencing and mapping to a
  reference.\n\nPrerequisites:\nThis workshop is intended for PhD students 
 and postdocs with a molecular biology background in (meta)genomics. Good u
 nderstanding of command line tools is a plus\, but not required. The 2nd d
 ay will offer an introduction to Linux and the command line.\n\nTools:\nmi
 nimap2\, pilon\, dorado\, porechop\, medaka\, quast\, metabat2\, Checkm2\,
  GTDBtk\, prokka\, bakta\, bwa2\, metagenomics-tk\n\nKeywords:\nNanopore s
 equencing\, genome assembly\, genomics\, metagenomics
SUMMARY:Nanopore Sequencing 101: From Library Prep to Genomics and Metageno
 mic Analysis
URL;VALUE=URI:https://www.denbi.de/training-courses-2026/2071-nanopore-sequ
 encing-101-from-library-prep-to-genomics-and-metagenomic-analysis
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