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DTSTAMP:20260810T155659Z
UID:0627d249-cad5-4bed-b7a9-6417636623c4
DTSTART:20250602T070000Z
DTEND:20250603T150000Z
DESCRIPTION:Educators:\nJochen Blom\, Oliver Schwengers\, Oliver Rupp (BiGi
 )\n\nDate:\n02.06.2025 – 03.06.2025\n\nLocation:\nJustus Liebig Universi
 ty Giessen\, Seltersweg 85\, Bioinformatics Lab\n\nContents:\nTopic of thi
 s two-day-workshop will be sequence data analysis of microbial genomes. Th
 is will include quality control\, assembly\, genome annotation and compara
 tive genomics using standard bioinformatics software tools (FastQC\, SPAde
 s\, Unicycler) and the de.NBI software tools like the annotation tool Bakt
 a and the comparative genomics platform EDGAR. Furthermore\, we will prese
 nt our new standardized bacterial sequence information repository BakRep\,
  and we will give a short introduction on the quick and easy submission of
  validated genome data to INSDC databases.\n\nThe two-day-course will be s
 eparated in three sessions\, session I in the afternoon of day one and ses
 sion II and III in the morning and afternoon of day two\, respectively.\n\
 nSession I will cover the field of genome assembly\, the reconstruction of
  the genomic DNA sequence from sequencing reads. This session gives an int
 roduction to the main concepts\, algorithms and tools for de novo genome a
 ssemblies. The course also focuses on the quality assessment of the sequen
 cing data and introduces quality metrics to compare different assembly res
 ults. The participants will gain practical experiences in a hands-on sessi
 on. Assembly methods for short reads and long reads will be covered.\n\nQA
 /QC of raw sequencing data\nAssembly concepts and algorithms\nQA/QC of ass
 embled genomes\nHands-on Computing assemblies\nIn session II\, the basic p
 rinciples of regional and functional genome annotation will be introduced\
 , and available tools and algorithms for the different annotation steps wi
 ll be explained. The de.NBI software tool Bakta for high-quality but never
 theless fast bacterial genome annotation will be presented in detail.\n\nT
 he basic principles of regional and functional annotations\nBacterial geno
 me annotation with Bakta\nHands-on examples via web and command-line inter
 faces\nFurthermore\, we will present our new large-scale bacterial genome 
 repository BakRep. We will explain the various contents of this repository
  and showcase how to use this for interactive bacterial genome screenings 
 followed by large-scale batch downloads for downstream analyses.\n\nFinall
 y\, there will be a short introduction into genome submission to INSDC seq
 uence databases. We will demonstrate how to prepapre\, validate\, and subm
 it genome sequences to the ENA database by using the tool Webin-CLI.\n\nIn
  session III\, the EDGAR platform for comparative genomics will be introdu
 ced. One main topic will be its use for phylogenetic analyses based on gen
 ome similarity indices and the complete core genome of organisms. All feat
 ures of EDGAR will be introduced in detail.\n\nGenomic subsets (core-genom
 e\, pan-genome\, singleton genes)\nCore-genome-based phylogenetic analyses
 \nANI\, AAI\, POCP\nStatistical analyses (core/pan/singleton development p
 lots)\nComparison of functional classifications (KEGG\, COG\, GO)\nThe pub
 lic EDGAR database\nAfter the EDGAR presentation\, there will be time for 
 custom data analysis consulting. Participants with own data which needs to
  be analyzed are encouraged to discuss their projects with the bioinformat
 ics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinfo
 rmatics (BiGi).\n\nIn all sessions\, the program includes hands-on trainin
 g to allow participants to become familiar with the presented software.\n\
 nLearning goals:\nPrinciples of computational sequence analysis\, hands-on
  experience with de.NBI/NFDI software services\n\nPrerequisites:\n-\n\nKey
 words:\nSequence data analysis\, genome assembly\, genomics\, annotation\,
  comparative genomics\, phylogenetic analysis\n\nTools:\nFastQC\, SPAdes\,
  Unicycler\, Bakta\, BakRep\, Webin-CLI\, EDGAR
LOCATION:Gießen
SUMMARY:9th Microbial Genomics training course
URL;VALUE=URI:https://www.denbi.de/training-courses-2025/1880-9th-microbial
 -genomics-training-course
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