{"id":188,"date":"2020-11-10T11:59:54","date_gmt":"2020-11-10T16:59:54","guid":{"rendered":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/?page_id=188"},"modified":"2022-07-23T09:07:21","modified_gmt":"2022-07-23T13:07:21","slug":"bioinformatics-modules","status":"publish","type":"page","link":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/research-projects\/faculty-admin\/faculty\/bioinformatics\/bioinformatics-modules\/","title":{"rendered":"Bioinformatics Modules"},"content":{"rendered":"

Because the window video player does not support other formats we suggest that faculty and students download VLC from the link below.\u00a0 It is free and open source. https:\/\/www.videolan.org\/vlc\/<\/a><\/strong><\/p>\n


\nI. Introduction:<\/strong><\/span><\/p>\n

    \n
  1. Introduction to Genomics and Bioinformatics modules<\/a><\/li>\n
  2. Principles of genomics<\/a><\/li>\n
  3. Generation of genomic data: NGS sequencing<\/a><\/li>\n
  4. Data structures and conventions<\/a><\/li>\n
  5. Sequencing and assembling a genome<\/a><\/li>\n
  6. Genome annotation and inferring function<\/a><\/li>\n<\/ol>\n

    II. Getting started<\/strong><\/span><\/p>\n

      \n
    1. Logging onto the Server<\/a><\/li>\n<\/ol>\n

      III. \u201cCommand Line\u201d tools:<\/strong><\/span><\/p>\n

        \n
      1. Anatomy of a Command<\/a><\/li>\n
      2. Finding Help<\/a><\/li>\n
      3. Pathways and Directories<\/a><\/li>\n
      4. Moving About<\/a><\/li>\n
      5. Move, Copy and Delete<\/a><\/li>\n
      6. Odds and Ends<\/a><\/li>\n
      7. Edit and View Files w\/ Nano<\/a><\/li>\n
      8. Search and Manipulate Files (grep)<\/a><\/li>\n
      9. Redirecting Standard Out<\/a><\/li>\n
      10. Wildcards and Globbing<\/a><\/li>\n
      11. Variables and parameter substitution<\/a><\/li>\n
      12. .Bashrc<\/a><\/li>\n
      13. File permissions<\/a><\/li>\n
      14. Shell Scripts<\/a><\/li>\n
      15. Nohup<\/a><\/li>\n<\/ol>\n

        IV. Assembling and annotating a genome:<\/strong><\/span><\/p>\n

          \n
        1. Trimmomatic: Data QC<\/a><\/li>\n
        2. SPADeS: assembling a genome<\/a><\/li>\n
        3. QUAST: assembly Metrics<\/a><\/li>\n
        4. Prokka: Annotating a genome<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

          Because the window video player does not support other formats we suggest that faculty and students download VLC from the link below.\u00a0 It is free and open source. https:\/\/www.videolan.org\/vlc\/ I. Introduction: Introduction to Genomics and Bioinformatics modules Principles of genomics Generation of genomic data: NGS sequencing Data structures and conventions [\u2026] <\/p>\n

          <\/div>\n

          Read More<\/a><\/p>\n","protected":false},"author":141,"featured_media":0,"parent":172,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-188","page","type-page","status-publish","hentry","author-141"],"jetpack_shortlink":"https:\/\/wp.me\/PbtsZW-32","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/pages\/188","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/users\/141"}],"replies":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/comments?post=188"}],"version-history":[{"count":7,"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/pages\/188\/revisions"}],"predecessor-version":[{"id":1382,"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/pages\/188\/revisions\/1382"}],"up":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/pages\/172"}],"wp:attachment":[{"href":"https:\/\/geiselmed.dartmouth.edu\/nhinbre\/wp-json\/wp\/v2\/media?parent=188"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}