{"action":"closed","issue":{"url":"https://api.github.com/repos/torognes/vsearch/issues/161","repository_url":"https://api.github.com/repos/torognes/vsearch","labels_url":"https://api.github.com/repos/torognes/vsearch/issues/161/labels{/name}","comments_url":"https://api.github.com/repos/torognes/vsearch/issues/161/comments","events_url":"https://api.github.com/repos/torognes/vsearch/issues/161/events","html_url":"https://github.com/torognes/vsearch/issues/161","id":133072930,"number":161,"title":"Add options to filter sequences and consensus sequences","user":{"login":"fgvieira","id":1151762,"avatar_url":"https://avatars.githubusercontent.com/u/1151762?v=3","gravatar_id":"","url":"https://api.github.com/users/fgvieira","html_url":"https://github.com/fgvieira","followers_url":"https://api.github.com/users/fgvieira/followers","following_url":"https://api.github.com/users/fgvieira/following{/other_user}","gists_url":"https://api.github.com/users/fgvieira/gists{/gist_id}","starred_url":"https://api.github.com/users/fgvieira/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fgvieira/subscriptions","organizations_url":"https://api.github.com/users/fgvieira/orgs","repos_url":"https://api.github.com/users/fgvieira/repos","events_url":"https://api.github.com/users/fgvieira/events{/privacy}","received_events_url":"https://api.github.com/users/fgvieira/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/torognes/vsearch/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-02-11T19:56:11Z","updated_at":"2016-09-20T14:29:15Z","closed_at":"2016-09-20T14:29:15Z","body":"Hi all,\r\n\r\nI've only recently discovered VSEARCH but I must say, so far, I am pretty impressed... It is super fast and it seems to get the job done pretty well.\r\n\r\nRight now I am mostly interested on the clustering algorithm but there is no way to filter sequences based on proportion/number of masked bases (as these sequences will most probably not be part of any meaningful alignment) like there is for minimum size (--minseqlength).\r\n\r\nRegarding the consensus sequence, I've noticed that if I cluster a set sequences twice (sequentially) the two outputs are different. I guess this is because VSEARCH performs a single-pass clustering, but is there any reason why it wouldn't do more passes?\r\nIt would also be nice to have more control over the consensus output, like only doing a consensus if a minimum number of sequences are present, or filter output it by proportion of missing data.\r\n\r\ncheers,\r\nFGV\r\n"}}
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