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DTSTAMP:20260616T152539Z
UID:3020fb81-1b2a-4200-a24b-c5fcf100c635
DTSTART:20191023T090000Z
DTEND:20191025T170000Z
DESCRIPTION:Educators:\nJochen Blom\, Oliver Rupp\, Oliver Schwengers\, Seb
 astian Jaenicke (BiGi)\, Stefanie Glaeser\n\nDate:\n23.10.2019 – 25.10.2
 019\n\nLocation:\nJustus-Liebig-University Giessen\, Heinrich-Buff-Ring 58
 \, Room 0024a\n\nContents:\nTopic of this three-day-workshop will be seque
 nce data analysis including quality control\, assembly\, genome annotation
  and comparative genomics with a focus on microbial taxonomy and phylogeno
 mics and as the usage of the BiGi software tools ASA3P\, EDGAR\, and MGX.\
 n\n \nThe first day will give a comprehensive introduction to the primary 
 data management in sequencing projects. In this part tools for sequence an
 alysis available via the Galaxy-Server of BIGI will be in the focus of the
  workshop.\n    • Initial quality assessment and quality control of raw 
 sequencing data\n    • Data preparation\, filtering and quality trimming
 \n    • Assembly strategies for different datasets\n\nFurthermore\, the 
 basic principles of regional and functional annotation will be introduced\
 , and available tools and algorithms for the different annotation steps wi
 ll be explained. The ASA3P platform for high-throughput parallel genome an
 notation and its capabilities in antibiotic resistance and virulence facto
 r detection will be presented in detail.\n    • The basic principles of 
 regional and functional annotation\n    • Genome annotation pipelines fo
 r single and multiple genomes\n    • High throughput genome annotation u
 sing ASA3P\n\nThe second day will provide an introduction to the role of g
 enotypic methods in prokaryotic taxonomy including the 16S rRNA gene seque
 nce phylogeny and genome sequences in the identification of environmental 
 isolates. It will will also demonstrate the use of genome sequences to exp
 lore the functions of those isolates.\n\n    • The basic role of 16S rRN
 A gene sequences in Prokaryotic identification in taxonomic and ecology\n 
    • Concept of the phylogenetic analysis of environmental 16S rRNA gene
  amplicon datasets (introduction of SilvaNGS)\n    • Current role of gen
 ome sequences in species identification\n\nSubsequently the EDGAR platform
  for comparative genomics will be introduced. One main topic will be its u
 se for phylogenetic analyses based on genome similarity indices and the co
 mplete core genome of organisms. All features of EDGAR will be introduced 
 in detail.\n    • Genomic subset calculations (core-genome\, pan-genome\
 , singleton genes)\n    • Core-genome-based phylogenetic analyses\n    
 • Core genome based phylogeny\n        ◦ ANI\, AAI\, GGDC\n    • Sta
 tistical analyses (core/pan/singleton development plots)\n    • The publ
 ic EDGAR database\n\nThe third day will show solutions for whole genome sh
 otgun metagenomics. mWGS metagenomics has the potential to address the ful
 l spectra of genome-based issues. The focus here will be on taxonomic and 
 functional analysis with the aid of different bioinformatic tools. The sof
 tware solution MGX\, an integrated platform for metagenome analysis and da
 ta visualization\, will be demonstrated as comprehensive platform for read
 -based  metagenome analysis.\n    • The basic principles of metagenome a
 nalysis\n    • Available pipelines for taxonomic and functional analysis
 \n    • Statistical features: PCA\, PCoA\, Rarefaction\, …\n\nThe afte
 rnoon of the third day will be kept free for custom data analysis consulti
 ng. Participants are encouraged to bring their own data which can be discu
 ssed with the bioinformatics experts of the Bielefeld-Gießen Resource Cen
 ter for Microbial Bioinformatics (BiGi).\n\nOn all three days the program 
 includes extensive hands-on training to allow participants to become famil
 iar with the presented software.\n\nLearning goals:\nPrinciples of computa
 tional sequence analysis\, hands-on experience with de.NBI software servic
 es\n\nPrerequisites:\nNone\n\nKeywords:\nSequence data analysis\, genomics
 \, annotation\, comparative genomics\, phylogenetic analysis\, metagenome 
 analysis\n\nTools:\nGenDB\, ASA3P\, EDGAR\, MGX
LOCATION:Gießen
SUMMARY:Environmental Genomics training course 
URL;VALUE=URI:https://www.denbi.de/training/700-environmental-genomics-trai
 ning-course
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