{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/1344","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/1344/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/1344/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/1344/events","html_url":"https://github.com/vgteam/vg/pull/1344","id":284425512,"number":1344,"title":"Is progressive alignment in vg our only hope for building large pangenomes?","user":{"login":"ekg","id":145425,"avatar_url":"https://avatars1.githubusercontent.com/u/145425?v=4","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"labels":[{"id":280142072,"url":"https://api.github.com/repos/vgteam/vg/labels/in%20progress","name":"in progress","color":"ededed","default":false}],"state":"open","locked":false,"assignee":{"login":"ekg","id":145425,"avatar_url":"https://avatars1.githubusercontent.com/u/145425?v=4","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"assignees":[{"login":"ekg","id":145425,"avatar_url":"https://avatars1.githubusercontent.com/u/145425?v=4","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2017-12-25T09:00:36Z","updated_at":"2017-12-27T20:39:29Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/vgteam/vg/pulls/1344","html_url":"https://github.com/vgteam/vg/pull/1344","diff_url":"https://github.com/vgteam/vg/pull/1344.diff","patch_url":"https://github.com/vgteam/vg/pull/1344.patch"},"body":"I am working on building pangenomes from fully assembled genomes with collections of unplaced contigs. I will do this using vg as a workaround. Existing approaches ([progressiveCactus](https://github.com/glennhickey/progressiveCactus), [REVEAL](https://github.com/jasperlinthorst/reveal), [TwoPacCo](https://github.com/medvedevgroup/TwoPaCo)) have specific problems for my use that may be resolvable, but are beyond the scope of what I can immediately work on, specifically:\r\n\r\n- progressiveCactus produces an output that cannot be directly read into vg, and the conversion utility is pegged to an old version of vg\r\n- REVEAL produces DAG/MSA outputs with a specific trick used to detect inversions. Genomes I have been working with tend to have CNVs, and these won't be integrated directly.\r\n- TwoPaCo proposes a compacted deBruijn graph, but it is not clear if this is appropriate. Also, the graph encoding does not seem to match vg's.\r\n\r\nThis branch will aim to improve the runtime of msga on large genomes. Rather than following the \"full\" approach as in progressiveCactus, where we might align all chromosomes against all others, we can reduce the complexity and improve parallelism by aligning together only those sequences that are likely to be the same chromosome.\r\n\r\nUnplaced contigs may be clustered (somehow, I'm not sure yet) and aligned together in a similar way as applicable. Maybe using minhashing would be the way to go."},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/354174535","html_url":"https://github.com/vgteam/vg/pull/1344#issuecomment-354174535","issue_url":"https://api.github.com/repos/vgteam/vg/issues/1344","id":354174535,"user":{"login":"cgcloud-jenkins","id":12962446,"avatar_url":"https://avatars2.githubusercontent.com/u/12962446?v=4","gravatar_id":"","url":"https://api.github.com/users/cgcloud-jenkins","html_url":"https://github.com/cgcloud-jenkins","followers_url":"https://api.github.com/users/cgcloud-jenkins/followers","following_url":"https://api.github.com/users/cgcloud-jenkins/following{/other_user}","gists_url":"https://api.github.com/users/cgcloud-jenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/cgcloud-jenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cgcloud-jenkins/subscriptions","organizations_url":"https://api.github.com/users/cgcloud-jenkins/orgs","repos_url":"https://api.github.com/users/cgcloud-jenkins/repos","events_url":"https://api.github.com/users/cgcloud-jenkins/events{/privacy}","received_events_url":"https://api.github.com/users/cgcloud-jenkins/received_events","type":"User","site_admin":false},"created_at":"2017-12-27T20:39:29Z","updated_at":"2017-12-27T20:39:29Z","author_association":"NONE","body":"[Jenkins vg tests](http://jenkins.cgcloud.info/job/vg/1296/) complete for [PR 1344](https://github.com/vgteam/vg/pull/1344).  View the [full report here](http://cgl-pipeline-inputs.s3.amazonaws.com/vg_cgl/vg_ci/jenkins_reports/commit/e6efe87f35c9b92faf37375e2e5c9ce2aea0c9cd/index.html).\n\n17 tests passed, 0 tests failed and 11 tests skipped in 11704 seconds\n\nTests produced 3042 warnings. 3042 were for lower-than-expected alignment scores\n\n"}}
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