{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/dib-lab/issues/22","labels_url":"https://api.github.com/repos/dib-lab/dib-lab/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/dib-lab/issues/22/comments","events_url":"https://api.github.com/repos/dib-lab/dib-lab/issues/22/events","html_url":"https://github.com/dib-lab/dib-lab/issues/22","id":90450240,"number":22,"title":"Brainstorm on assembly graph comparison","user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-23T17:50:26Z","updated_at":"2015-06-23T17:59:36Z","closed_at":null,"body":"Suppose we can combine multiple assembly graphs and do comparisons between graph structure, label graphs well, etc. What are some reasons we would want to do this for, you know, biology purposes? (For #21)\r\n\r\nI have:\r\n\r\n* colored DBG stuff that @iqbal-lab has been doing;\r\n* faster/more efficient identification of differences (can we do this in a streaming fashion? probably)\r\n* fast discovery of identical and/or highly variable regions\r\n* graph-tagging and building of a correspondence structure to move quickly between homologous regions/proteins within and between assembly graphs;\r\n* overlay multiple pieces of evidence on a single graph and distinguish between them (e.g. what isoforms are supported by long reads? what splice junctions are supported by short reads?)\r\n* case/control comparisons (GWAS style separation of features directly on assembly graph)\r\n* take advantage of multiple low-coverage populations to do boosted assembly/variant discovery while retaining original identity/origin of sequence\r\n* label individual long reads (and even short reads) depending on optimization\r\n* overlay string-graph-style structure on a DBG"},"comment":{"url":"https://api.github.com/repos/dib-lab/dib-lab/issues/comments/114591196","html_url":"https://github.com/dib-lab/dib-lab/issues/22#issuecomment-114591196","issue_url":"https://api.github.com/repos/dib-lab/dib-lab/issues/22","id":114591196,"user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2015-06-23T17:59:36Z","updated_at":"2015-06-23T17:59:36Z","body":"* traverse multiple graphs simultaneously looking for polymorphisms/SNPs/variants; essentially, an extension of readaligner. (but for what purpose - multiple sequence alignment?\r\n* identify regions in one graph but not in another, quickly; graph subtraction, in effect.\r\n* have a \"no go list\" that blocks traversal in various ways (e.g. \"already been assembled\" or \"uninteresting\" or ...)"}}