{"action":"created","issue":{"url":"https://api.github.com/repos/lskatz/lyve-SET/issues/26","labels_url":"https://api.github.com/repos/lskatz/lyve-SET/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/lskatz/lyve-SET/issues/26/comments","events_url":"https://api.github.com/repos/lskatz/lyve-SET/issues/26/events","html_url":"https://github.com/lskatz/lyve-SET/issues/26","id":60354014,"number":26,"title":"\"Fast\" mode","user":{"login":"lskatz","id":14798,"avatar_url":"https://avatars.githubusercontent.com/u/14798?v=3","gravatar_id":"","url":"https://api.github.com/users/lskatz","html_url":"https://github.com/lskatz","followers_url":"https://api.github.com/users/lskatz/followers","following_url":"https://api.github.com/users/lskatz/following{/other_user}","gists_url":"https://api.github.com/users/lskatz/gists{/gist_id}","starred_url":"https://api.github.com/users/lskatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lskatz/subscriptions","organizations_url":"https://api.github.com/users/lskatz/orgs","repos_url":"https://api.github.com/users/lskatz/repos","events_url":"https://api.github.com/users/lskatz/events{/privacy}","received_events_url":"https://api.github.com/users/lskatz/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/lskatz/lyve-SET/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":{"login":"lskatz","id":14798,"avatar_url":"https://avatars.githubusercontent.com/u/14798?v=3","gravatar_id":"","url":"https://api.github.com/users/lskatz","html_url":"https://github.com/lskatz","followers_url":"https://api.github.com/users/lskatz/followers","following_url":"https://api.github.com/users/lskatz/following{/other_user}","gists_url":"https://api.github.com/users/lskatz/gists{/gist_id}","starred_url":"https://api.github.com/users/lskatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lskatz/subscriptions","organizations_url":"https://api.github.com/users/lskatz/orgs","repos_url":"https://api.github.com/users/lskatz/repos","events_url":"https://api.github.com/users/lskatz/events{/privacy}","received_events_url":"https://api.github.com/users/lskatz/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/lskatz/lyve-SET/milestones/3","html_url":"https://github.com/lskatz/lyve-SET/milestones/v3.0","labels_url":"https://api.github.com/repos/lskatz/lyve-SET/milestones/3/labels","id":994237,"number":3,"title":"v3.0","description":null,"creator":{"login":"lskatz","id":14798,"avatar_url":"https://avatars.githubusercontent.com/u/14798?v=3","gravatar_id":"","url":"https://api.github.com/users/lskatz","html_url":"https://github.com/lskatz","followers_url":"https://api.github.com/users/lskatz/followers","following_url":"https://api.github.com/users/lskatz/following{/other_user}","gists_url":"https://api.github.com/users/lskatz/gists{/gist_id}","starred_url":"https://api.github.com/users/lskatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lskatz/subscriptions","organizations_url":"https://api.github.com/users/lskatz/orgs","repos_url":"https://api.github.com/users/lskatz/repos","events_url":"https://api.github.com/users/lskatz/events{/privacy}","received_events_url":"https://api.github.com/users/lskatz/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":0,"state":"open","created_at":"2015-02-24T22:48:31Z","updated_at":"2015-03-09T14:49:09Z","due_on":null,"closed_at":null},"comments":1,"created_at":"2015-03-09T14:49:09Z","updated_at":"2015-03-12T19:47:45Z","closed_at":null,"body":"Make a workflow that takes shortcuts\r\n\r\n* only find SNPs in the most divergent genome and only call SNPs in those locations\r\n  * Not actually sure if this would make it faster\r\n* skip phage-finding\r\n* downsample genomes to 20 - 50x\r\n* Choose faster modules (e.g., SNAP)"},"comment":{"url":"https://api.github.com/repos/lskatz/lyve-SET/issues/comments/78590957","html_url":"https://github.com/lskatz/lyve-SET/issues/26#issuecomment-78590957","issue_url":"https://api.github.com/repos/lskatz/lyve-SET/issues/26","id":78590957,"user":{"login":"lskatz","id":14798,"avatar_url":"https://avatars.githubusercontent.com/u/14798?v=3","gravatar_id":"","url":"https://api.github.com/users/lskatz","html_url":"https://github.com/lskatz","followers_url":"https://api.github.com/users/lskatz/followers","following_url":"https://api.github.com/users/lskatz/following{/other_user}","gists_url":"https://api.github.com/users/lskatz/gists{/gist_id}","starred_url":"https://api.github.com/users/lskatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lskatz/subscriptions","organizations_url":"https://api.github.com/users/lskatz/orgs","repos_url":"https://api.github.com/users/lskatz/repos","events_url":"https://api.github.com/users/lskatz/events{/privacy}","received_events_url":"https://api.github.com/users/lskatz/received_events","type":"User","site_admin":false},"created_at":"2015-03-12T19:47:45Z","updated_at":"2015-03-12T19:47:45Z","body":"`--fast` was added in `set_test.pl` which makes it so that the reference genome is not simulated and is not included in the final tree.  Additionally, it passes `--fast` to `launch_set` which forces it to use `snap`, no masking of phages, and downsampling via `run_assembly_removeDuplicateReads.pl` to 50x using the reference genome as a guide for genome size.\r\n\r\nNeed to still implement selective SNP calling though."}}