{"action":"created","issue":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/105","repository_url":"https://api.github.com/repos/bcgsc/abyss","labels_url":"https://api.github.com/repos/bcgsc/abyss/issues/105/labels{/name}","comments_url":"https://api.github.com/repos/bcgsc/abyss/issues/105/comments","events_url":"https://api.github.com/repos/bcgsc/abyss/issues/105/events","html_url":"https://github.com/bcgsc/abyss/issues/105","id":149512296,"number":105,"title":"abyss-fatoagp outputs ultra-short contigs that are rejected during genbank submission","user":{"login":"benvvalk","id":1652775,"avatar_url":"https://avatars.githubusercontent.com/u/1652775?v=3","gravatar_id":"","url":"https://api.github.com/users/benvvalk","html_url":"https://github.com/benvvalk","followers_url":"https://api.github.com/users/benvvalk/followers","following_url":"https://api.github.com/users/benvvalk/following{/other_user}","gists_url":"https://api.github.com/users/benvvalk/gists{/gist_id}","starred_url":"https://api.github.com/users/benvvalk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benvvalk/subscriptions","organizations_url":"https://api.github.com/users/benvvalk/orgs","repos_url":"https://api.github.com/users/benvvalk/repos","events_url":"https://api.github.com/users/benvvalk/events{/privacy}","received_events_url":"https://api.github.com/users/benvvalk/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/bcgsc/abyss/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"benvvalk","id":1652775,"avatar_url":"https://avatars.githubusercontent.com/u/1652775?v=3","gravatar_id":"","url":"https://api.github.com/users/benvvalk","html_url":"https://github.com/benvvalk","followers_url":"https://api.github.com/users/benvvalk/followers","following_url":"https://api.github.com/users/benvvalk/following{/other_user}","gists_url":"https://api.github.com/users/benvvalk/gists{/gist_id}","starred_url":"https://api.github.com/users/benvvalk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benvvalk/subscriptions","organizations_url":"https://api.github.com/users/benvvalk/orgs","repos_url":"https://api.github.com/users/benvvalk/repos","events_url":"https://api.github.com/users/benvvalk/events{/privacy}","received_events_url":"https://api.github.com/users/benvvalk/received_events","type":"User","site_admin":false},"milestone":null,"comments":5,"created_at":"2016-04-19T16:26:22Z","updated_at":"2016-04-19T17:49:00Z","closed_at":null,"body":"It has been reported to me that:\r\n\r\nWhen the sequences between stretches of \"N\"s is short (e.g. 1 base), `abyss-fatoagp` will generate short contigs in the output AGP file that are rejected during submission to genbank.   The suggested solution is to add a new minimum contig length parameter and mask scaftigs shorter than this threshold with \"N\"s before splitting to AGP."},"comment":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/comments/212038834","html_url":"https://github.com/bcgsc/abyss/issues/105#issuecomment-212038834","issue_url":"https://api.github.com/repos/bcgsc/abyss/issues/105","id":212038834,"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":"2016-04-19T17:49:00Z","updated_at":"2016-04-19T17:49:00Z","body":"Do you know whether it was due to the PathConsensus consensus sequence issue or the k-mer-sized-contig issue?"}}