BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260407T181206Z UID:cd2f4a57-ace1-44ce-8573-35692806cb92 DTSTART:20260624T100000Z DTEND:20260626T120000Z DESCRIPTION:Educators\nJochen Blom\, Oliver Schwengers\, Oliver Rupp (BiGi) \n\nDate\n24.06.2026-26.06.2026\n\nLocation\nJustus Liebig University Gies sen\, Seltersweg 85\, Bioinformatics Lab\n\nContents\nTopic of this three- day-workshop will be whole-genome sequence data analysis of microbial geno mes. This will include quality control\, assembly\, genome annotation and comparative genomics using standard bioinformatics software tools (FastQC\ , FastP\, SPAdes\, Unicycler\, Flye) and the de.NBI software tools like th e annotation tool Bakta and the comparative genomics platform EDGAR. Furth ermore\, we will present our new standardized bacterial sequence informati on repository BakRep\, and we will give a short introduction on the quick and easy submission of validated genome data to INSDC databases.\n\nThe th ree-day-course will be separated into five sessions. Session I in the afte rnoon of day one\, session II and III\, and session IV and V in the mornin g and afternoon of day two and three\, respectively.\n\nSession I will pro vide a general introduction into the field of genome assembly\, the recons truction of the genomic DNA sequence from sequencing reads. This session g ives an introduction to the main concepts\, algorithms and tools\, and pec uliarities for de novo genome assemblies using short and long read sequenc ing reads. The course also focuses on the quality assessment of the sequen cing data and introduces quality metrics to compare different assembly res ults. \n\nIn session II\, the participants will gain practical experiences in a hands-on session. Assembly methods for short reads and long reads wi ll be covered.\n\nQA/QC of raw sequencing data\nAssembly concepts and algo rithms\nQA/QC of assembled genomes\nHands-on Computing assemblies\nIn sess ion III\, the basic principles of regional and functional genome annotatio n will be introduced\, and available tools and algorithms for the differen t annotation steps will be explained. The de.NBI software tool Bakta for h igh-quality but nevertheless fast bacterial genome annotation will be pres ented in detail.\n\nThe basic principles of regional and functional annota tions\nBacterial genome annotation with Bakta\nHands-on examples via web a nd command-line interfaces\nFurthermore\, we will present our new large-sc ale bacterial genome repository BakRep. We will explain the various conten ts of this repository and showcase how to use this for interactive bacteri al genome screenings followed by large-scale batch downloads for downstrea m analyses.\n\nIn session IV\, there will be a short introduction into gen ome submission to INSDC sequence databases. We will demonstrate how to pre pare\, validate\, and submit genome sequences to the ENA database by using the tool Webin-CLI. Afterwards\, the EDGAR platform for comparative genom ics will be introduced. One main topic will be its use for phylogenetic an alyses based on genome similarity indices and the complete core genome of organisms. All features of EDGAR will be introduced in detail\n\nGenomic s ubsets (core-genome\, pan-genome\, singleton genes)\nCore-genome-based phy logenetic analyses\nANI\, AAI\, POCP\nStatistical analyses (core/pan/singl eton development plots)\nComparison of functional classifications (KEGG\, COG\, GO)\nThe public EDGAR database\nIn session V\, the participants will gain practical experience in a hands-on session. All aspects of the EDGAR platform will be covered and features of EDGAR will be show-cased in deta il.\n\nLast but not least\, there will be a wrap-up to discuss the present ed tools and workflow and participants are encouraged to discuss open ques tions and practical issues. \n\nFollowing all afternoon sessions\, there w ill be time for custom data analysis consulting. Participants are encourag ed to bring their own data which needs to be analyzed and/or discussed wit h the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi).\n\nIn all sessions\, the program includes hands-on training to allow participants to become familiar with the prese nted software.\n\nAgenda:\n\nWednesday (24.06.2026): \nAfternoon session: Genome assembly (Oliver Rupp)\n12:00 – 13:00 Arrival of participants\n 13:00 – 13:15 Welcome &\; introduction\n13:15 – 14:30 Introduct ion to genome assembly Part 1 - Assembly basics\n14:30 – 15:00 Coffee B reak\n15:00 – 16:30 Introduction to genome assembly Part 1 - Assembly s trategies (short reads\, long reads and hybrid)\n\nThursday (25.06.2026): \nMorning session: Genome assembly hands on (Oliver Rupp)\n09:00 – 10:3 0 Genome assembly hands on Part 1\n10:30 – 11:00 Coffee Break\n11:00 – 12:00 Genome assembly hands on Part 2\n12:00 – 13:00 Lunch\n\nAf ternoon session: Genome annotation (Oliver Schwengers)\n13:00 – 15:00 Introduction to genome annotation \n15:00 – 15:30 Coffee Break\n15:30 – 16:30 Bacta hands on\n\nFriday (26.06.2026): \nMorning session: Com parative Genomics (Jochen Blom)\n09:00 – 09:45 NCBI/ENA genome submissi on \n09:45 – 10:00 Coffee Break\n10:00 – 12:00 Introduction to EDG AR platform\n12:00 – 13:00 Lunch\n\nAfternoon session: Comparative Gen omics (Jochen Blom)\n13:00 – 14:00 EDGAR Hands on \n14:00 – 14:30 Wrap-up and goodbye\n\nLearning goals:\nPrinciples of computational sequen ce analysis\, hands-on experience with de.NBI/NFDI software services\n\nPr erequisites:\n-\n\nKeywords:\nSequence data analysis\, genome assembly\, g enomics\, annotation\, comparative genomics\, phylogenetic analysis\n\nToo ls:\nFastQC\, SPAdes\, Unicycler\, Bakta\, BakRep\, Webin-CLI\, EDGAR LOCATION:Seltersweg 85\, 85 Seltersweg SUMMARY:10th Microbial Genomics training course URL;VALUE=URI:https://www.denbi.de/training-courses-2026/2057-10th-microbia l-genomics-training-course END:VEVENT END:VCALENDAR