{"action":"created","issue":{"url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/8","labels_url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/8/comments","events_url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/8/events","html_url":"https://github.com/pmelsted/GFA-spec/issues/8","id":98559948,"number":8,"title":"Example of the graph representation used in Falcon","user":{"login":"pb-jchin","id":1071734,"avatar_url":"https://avatars.githubusercontent.com/u/1071734?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-jchin","html_url":"https://github.com/pb-jchin","followers_url":"https://api.github.com/users/pb-jchin/followers","following_url":"https://api.github.com/users/pb-jchin/following{/other_user}","gists_url":"https://api.github.com/users/pb-jchin/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-jchin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-jchin/subscriptions","organizations_url":"https://api.github.com/users/pb-jchin/orgs","repos_url":"https://api.github.com/users/pb-jchin/repos","events_url":"https://api.github.com/users/pb-jchin/events{/privacy}","received_events_url":"https://api.github.com/users/pb-jchin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-08-01T20:30:00Z","updated_at":"2015-08-03T18:34:19Z","closed_at":null,"body":"Just for a reference.  The basic graph I use in the FALCON assembler (https://github.com/PacificBiosciences/FALCON/) is very straigh forward. I decouple the graph information from the sequences information. The sequences used in the graph is just referenced from the text file `sg_edges_list`. Here is a simple example and some brief description: \r\n\r\n```\r\n$ head -5 sg_edges_list\r\n000017363:B 000007817:E 000007817 10841 28901 10841 99.52 TR\r\n000015379:E 000004331:B 000004331 6891 0 18178 99.35 TR\r\n000006813:B 000000681:E 000000681 7609 23795 7616 99.72 TR\r\n000002258:E 000002505:B 000002505 5850 0 17215 99.62 TR\r\n000013449:B 000012565:B 000012565 3317 0 20570 99.72 G\r\n```\r\n\r\nThe first two columns indicates the in and out node of the edge. The node notation contain two files operated by :. The first field is the read identifier. The second field is either B or E. B is the 5' end of the read and E is the 3' end of the reads. The next three field indicates the corresponding sequences of the edges. In this example, the edge in the first line contains the sequence from read 000007817 base [10841, 28901). If the second coordinate is smaller than the first one, it means the corresponded sequence is reverse complimented. The next two column are the number of overlapped base and the overlap identity. The final column is the classification. Currently, there are 4 different types G, TR, R, and S. An edge with type \"G\" is used for the final string graph. A \"TR\" means the edge is transitive reducible. \"R\" means the edge is removed during the local repeat resolution and \"S\" means the edge is likely to be a \"spur\" which only one ends is connected.\r\n\r\nIt won't be too hard to convert such information @lh3's original proposal for GFA which label's sequnces ends rather than the seqments themselves.\r\n\r\n Here is an example to compare the different graphs using three reads as an example:\r\nhttps://github.com/pb-jchin/GFA-spec/blob/master/examples/ThreeReads_Summary.svg"},"comment":{"url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/comments/127364207","html_url":"https://github.com/pmelsted/GFA-spec/issues/8#issuecomment-127364207","issue_url":"https://api.github.com/repos/pmelsted/GFA-spec/issues/8","id":127364207,"user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"created_at":"2015-08-03T18:34:19Z","updated_at":"2015-08-03T18:34:19Z","body":"Exonerate uses the `+` and `-` characters for this purpose. I'm used to it, and I do like it in fact."}}