{"action":"created","issue":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/266","repository_url":"https://api.github.com/repos/ewels/MultiQC","labels_url":"https://api.github.com/repos/ewels/MultiQC/issues/266/labels{/name}","comments_url":"https://api.github.com/repos/ewels/MultiQC/issues/266/comments","events_url":"https://api.github.com/repos/ewels/MultiQC/issues/266/events","html_url":"https://github.com/ewels/MultiQC/issues/266","id":165601863,"number":266,"title":"add support for quast, assembly assessment","user":{"login":"flashton2003","id":2613906,"avatar_url":"https://avatars.githubusercontent.com/u/2613906?v=3","gravatar_id":"","url":"https://api.github.com/users/flashton2003","html_url":"https://github.com/flashton2003","followers_url":"https://api.github.com/users/flashton2003/followers","following_url":"https://api.github.com/users/flashton2003/following{/other_user}","gists_url":"https://api.github.com/users/flashton2003/gists{/gist_id}","starred_url":"https://api.github.com/users/flashton2003/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flashton2003/subscriptions","organizations_url":"https://api.github.com/users/flashton2003/orgs","repos_url":"https://api.github.com/users/flashton2003/repos","events_url":"https://api.github.com/users/flashton2003/events{/privacy}","received_events_url":"https://api.github.com/users/flashton2003/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ewels/MultiQC/labels/module:%20new","name":"module: new","color":"bfe5bf"}],"state":"open","locked":false,"assignee":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"assignees":[{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/ewels/MultiQC/milestones/6","html_url":"https://github.com/ewels/MultiQC/milestones/Module%20Backlog","labels_url":"https://api.github.com/repos/ewels/MultiQC/milestones/6/labels","id":1449577,"number":6,"title":"Module Backlog","description":"Backlog of requested modules. Feature requests should be added to this milestone, then moved to a concrete milestone when planned.","creator":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"open_issues":6,"closed_issues":7,"state":"open","created_at":"2015-12-08T10:22:00Z","updated_at":"2016-07-14T21:13:32Z","due_on":null,"closed_at":null},"comments":4,"created_at":"2016-07-14T16:20:39Z","updated_at":"2016-07-18T13:38:29Z","closed_at":null,"body":"\r\n- quast is a really useful tool for assessing de novo assemblies against reference genomes, http://quast.bioinf.spbau.ru/\r\n- i think they include some test data in the install\r\n- personally, i think N50, total length, number misassemblies, number mismatches, indels, genes (if -G is given), genome fraction are the most important.\r\n- they do some plots, i'm not 100% convinced how usful they are, but ymmv\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/comments/233330637","html_url":"https://github.com/ewels/MultiQC/issues/266#issuecomment-233330637","issue_url":"https://api.github.com/repos/ewels/MultiQC/issues/266","id":233330637,"user":{"login":"flashton2003","id":2613906,"avatar_url":"https://avatars.githubusercontent.com/u/2613906?v=3","gravatar_id":"","url":"https://api.github.com/users/flashton2003","html_url":"https://github.com/flashton2003","followers_url":"https://api.github.com/users/flashton2003/followers","following_url":"https://api.github.com/users/flashton2003/following{/other_user}","gists_url":"https://api.github.com/users/flashton2003/gists{/gist_id}","starred_url":"https://api.github.com/users/flashton2003/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flashton2003/subscriptions","organizations_url":"https://api.github.com/users/flashton2003/orgs","repos_url":"https://api.github.com/users/flashton2003/repos","events_url":"https://api.github.com/users/flashton2003/events{/privacy}","received_events_url":"https://api.github.com/users/flashton2003/received_events","type":"User","site_admin":false},"created_at":"2016-07-18T13:38:29Z","updated_at":"2016-07-18T13:38:29Z","body":"Ah, I think I see the source of our confusion. The example quast tsv has multiple columns, but typically, in my usage, there is only one sample per file. See two attached examples.\r\n\r\n14892_1.2report.txt is a bad assembly, the other two are ok.\r\n\r\n[14892_1#16_report.txt](https://github.com/ewels/MultiQC/files/369116/14892_1.16_report.txt)\r\n\r\n[14892_1#2report.txt](https://github.com/ewels/MultiQC/files/369100/14892_1.2report.txt)\r\n\r\n[14892_1#15_report.txt](https://github.com/ewels/MultiQC/files/369099/14892_1.15_report.txt)\r\n\r\nI think the multiple samples in the tsv are a result of running quast on multiple samples at once i.e. `quast.py <options> contigs1.fasta contigs2.fasta` whereas I ran quast on each sample individually, then combined outputs for analysis. \r\n\r\nThe combined quast output is already quite good, so not sure if this will be the most 'bang for your buck' in terms of adding to multiqc, but I still think it would be good to have it within multiqc. Example of combined report in html is below (github doesn't let attach html files).\r\n\r\nhttps://www.dropbox.com/s/rw9guhsec6zbet8/report.html?dl=0\r\n"}}
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