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DTSTAMP:20260617T054201Z
UID:97629f56-5912-4b32-ab54-623550f4551a
DTSTART:20231211T080000Z
DTEND:20231212T160000Z
DESCRIPTION:Educators:\nJochen Blom\, Oliver Schwengers\, Oliver Rupp (BiGi
 )\n\nDate:\n11.12.2023 – 12.12.2023\n\nLocation:\nJustus Liebig Universi
 ty Giessen\, Heinrich-Buff-Ring 58\, Room 0024a\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 short sequencing reads. This session gives 
 an introduction to the main concepts\, algorithms and tools for de novo ge
 nome assemblies. The course also focuses on the quality assessment of the 
 sequencing data and introduces quality metrics to compare different assemb
 ly results. The participants will gain practical experiences in a hands-on
  session using the Galaxy platform.\n\nQA/QC of raw sequencing data\nAssem
 bly concepts and algorithms\nQA/QC of assembled genomes\nComputing assembl
 ies with Galaxy\nIn session II\, the basic principles of regional and func
 tional annotation will be introduced\, and available tools and algorithms 
 for the different annotation steps will be explained. The de.NBI software 
 tool Bakta for high-quality but nevertheless fast bacterial genome annotat
 ion will be presented in detail.\n\nThe basic principles of regional and f
 unctional annotations\nBacterial genome annotation with Bakta\nHands-on ex
 amples via web and command-line interfaces\nFurthermore\, we will present 
 our new large-scale bacterial genome repository BakRep. We will explain th
 e various contents of this repository and showcase how to use this for int
 eractive bacterial genome screenings followed by large-scale batch downloa
 ds for downstream analyses.\n\nFinally\, there will be a short introductio
 n on how to validate and submit genome sequences to the ENA database by us
 ing the Webin Command line tool.\n\nIn session III\, the EDGAR platform fo
 r comparative genomics will be introduced. One main topic will be its use 
 for phylogenetic analyses based on genome similarity indices and the compl
 ete core genome of organisms. All features of EDGAR will be introduced in 
 detail.\n\nGenomic subsets (core-genome\, pan-genome\, singleton genes)\nC
 ore-genome-based phylogenetic analyses\nANI\, AAI\, POCP\nStatistical anal
 yses (core/pan/singleton development plots)\nComparison of functional clas
 sifications (KEGG\, COG\, GO)\nThe public EDGAR database\nAfter the EDGAR 
 presentation\, there will be time for custom data analysis consulting. Par
 ticipants with own data which needs to be analyzed are encouraged to discu
 ss their projects with the bioinformatics experts of the Bielefeld-Gießen
  Resource Center for Microbial Bioinformatics (BiGi).\n\nIn all sessions\,
  the program includes extensive hands-on training to allow participants to
  become familiar with the presented software.\n\nLearning goals:\nPrincipl
 es of computational sequence analysis\, hands-on experience with de.NBI/NF
 DI software services\n\nPrerequisites:\n-\n\nKeywords:\nSequence data anal
 ysis\, genome assembly\, genomics\, annotation\, comparative genomics\, ph
 ylogenetic analysis\n\nTools:\nFastQC\, SPAdes\, Unicycler\, Bakta\, BakRe
 p\, Webin-CLI\, EDGAR
LOCATION:Heinrich-Buff-Ring 58\, 58 Heinrich-Buff-Ring
SUMMARY:8th de.NBI Genomics training course
URL;VALUE=URI:https://www.denbi.de/training/1655-8th-de-nbi-genomics-traini
 ng-course
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