{"id":2093,"date":"2021-04-22T12:48:49","date_gmt":"2021-04-22T11:48:49","guid":{"rendered":"https:\/\/med.st-andrews.ac.uk\/staahr\/?page_id=2093"},"modified":"2021-04-22T12:48:49","modified_gmt":"2021-04-22T11:48:49","slug":"genome-analysis-workshop","status":"publish","type":"page","link":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/education-and-training\/genome-analysis-workshop\/","title":{"rendered":"Genome Analysis Workshop, April 2021"},"content":{"rendered":"

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Genome Analysis Workshop, April 2021<\/h1>\n

\"\"<\/strong><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”3_4,1_4″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_column type=”3_4″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_text admin_label=”Intro Text” _builder_version=”4.9.10″ _module_preset=”default” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n

Hands-on training in examining whole genomes of UTI-causing bacteria collected from HATUA sites using Galaxy Europe interface and relevant platforms used in bioinformatics.<\/strong><\/p>\n

 <\/p>\n

Learning Outcomes<\/h4>\n

By the end of the training, you should be able to:<\/p>\n

    \n
  1. Examine high-throughput molecular data using tools installed in Galaxy Europe and other relevant platforms.<\/li>\n
  2. Predict AMR content, transmission and evolution within bacterial genomes and apply the principles in HATUA sample collections.<\/li>\n
  3. Reconstruct evolutionary relationships between HATUA genomes of the same species using phylogenetic trees and link these to clinical and other HATUA data types.<\/li>\n<\/ol>\n

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    Week<\/strong><\/td>\nDates Covered<\/strong><\/td>\nConcepts<\/strong><\/td>\nHands-on<\/strong><\/td>\n<\/tr>\n
    1<\/td>\nApril 26-30<\/td>\nIntroduction to Genome sequencing, Genomics,HATUA.\u00a0 Bacterial genomics: AMR Evolution in bacteria.<\/td>\nIntroduction to Galaxy and R\/RStudio (swirl); Tools on Galaxy.\u00a0 Galaxy: Read library QC.<\/td>\n<\/tr>\n
    2<\/td>\nMay 03-07<\/td>\nGenome assembly and annotation; AMR Databases.<\/td>\nRead mapping; Assembling a genome from sequence data; Galaxy and Bandage: Annotating genomes with AMR genes and curating a HATUA AMR database; R\/RStudio data management.<\/td>\n<\/tr>\n
    3<\/td>\nTBC<\/td>\nSequence alignment and SNP calling, Phylogenetics and Phylogenomics.<\/td>\nGalaxy and R\/RStudio: How to discover and qualify single-nucleotide, copy number and chromosomal mutations; Tools for Comparative genomics and phylogenetics\/genomics (Microreact).<\/td>\n<\/tr>\n
    4<\/td>\nTBC<\/td>\nApplications of Genomics to public health research and epidemiology; Linking genomic data to other types of HATUA data.<\/td>\nData linkage in HATUA; Bonus: Tableau and iTol<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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    Week 1<\/h4>\n
      \n
    • Session 1<\/strong>: Introduction to Genomics and its application to HATUA study<\/li>\n
    • Session 2<\/strong>: Quick Guide on using Galaxy; Tools on Galaxy<\/li>\n
    • Session 3<\/strong>: Talk on the Pilot genome data analysis<\/li>\n
    • Session 4<\/strong>: Read library QC on Galaxy; Launching RStudio (swirl tutorial) on your Desktop and Galaxy<\/li>\n
    • Session 5<\/strong>: Worksheet instructions<\/li>\n<\/ul>\n

      Week 2<\/h4>\n
        \n
      • Session 1<\/strong>: Clinical data management in R\/RStudio (Guest: Ahmed Raza)<\/li>\n
      • Session 2<\/strong>: Genome assembly and annotation: Piecing the puzzle together and AMR gene hunting<\/li>\n
      • Session 3<\/strong>: Assessing Genome Quality using Quast; Viewing genomes on Bandage<\/li>\n
      • Session 4<\/strong>: Creating and executing workflows on Galaxy<\/li>\n
      • Session 5<\/strong>: Worksheet instructions<\/li>\n<\/ul>\n

        Week 3<\/h4>\n
          \n
        • Session 1<\/strong>: Sequence alignment, SNP calling, Phylogenetics\/genomics and Pangenomics<\/li>\n
        • Session 2<\/strong>: Phylogenetic reconstruction and visualisation on Galaxy and Figtree<\/li>\n
        • Session 3<\/strong>: Epidemiological studies using Microreact<\/li>\n
        • Session 4<\/strong>: Resolving pandemics using genomics (Guest: Prof. Matt Holden)<\/li>\n
        • Session 5<\/strong>: Worksheet instructions<\/li>\n<\/ul>\n

          Week 4<\/h4>\n
            \n
          • Session 1<\/strong>: From the terminal to the clinic (Guest: Martin McHugh)<\/li>\n
          • Session 2<\/strong>: Holistic data linkage in HATUA (Guest: Dominique Green)<\/li>\n
          • Session 3<\/strong>: Bonus tools — iTol and Tableau<\/li>\n
          • Session 4<\/strong>: Poster presentations<\/li>\n<\/ul>\n

            [\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,1_3,1_3″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_column type=”1_3″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_text admin_label=”Datasets” _builder_version=”4.9.2″ _module_preset=”default”]<\/p>\n

            Datasets<\/h4>\n
              \n
            1. HATUA Pilot genomes<\/li>\n
            2. Newly-released HATUA genome samples from MicrobesNG<\/li>\n
            3. Published WGS datasets<\/li>\n<\/ol>\n

              [\/et_pb_text][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_text admin_label=”Outputs” _builder_version=”4.9.2″ _module_preset=”default”]<\/p>\n

              Outputs<\/h4>\n
                \n
              1. Completed worksheets<\/li>\n
              2. Written summary report<\/li>\n
              3. One-page digital poster<\/li>\n<\/ol>\n

                [\/et_pb_text][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.9.2″ _module_preset=”default”][et_pb_text admin_label=”Abbreviations” _builder_version=”4.9.2″ _module_preset=”default”]<\/p>\n

                Abbreviations<\/h4>\n

                AMR<\/strong>: Antimicrobial resistance
                UTI<\/strong>: Urinary tract infection\/s
                QC<\/strong>: Quality control
                SNP<\/strong>: Single nucleotide polymorphism<\/p>\n

                [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

                Genome Analysis Workshop, April 2021 Hands-on training in examining whole genomes of UTI-causing bacteria collected from HATUA sites using Galaxy Europe interface and relevant platforms used in bioinformatics.   Learning Outcomes By the end of the training, you should be able to: Examine high-throughput molecular data using tools installed in Galaxy Europe and other relevant […]<\/p>\n","protected":false},"author":126,"featured_media":0,"parent":61,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-2093","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/pages\/2093","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/users\/126"}],"replies":[{"embeddable":true,"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/comments?post=2093"}],"version-history":[{"count":0,"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/pages\/2093\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/pages\/61"}],"wp:attachment":[{"href":"https:\/\/medicine.st-andrews.ac.uk\/staahr\/wp-json\/wp\/v2\/media?parent=2093"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}