{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/1962","labels_url":"https://api.github.com/repos/biocore/qiime/issues/1962/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/1962/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/1962/events","html_url":"https://github.com/biocore/qiime/issues/1962","id":63288712,"number":1962,"title":"Would like support for vsearch (open source)","user":{"login":"alk224","id":4246886,"avatar_url":"https://avatars.githubusercontent.com/u/4246886?v=3","gravatar_id":"","url":"https://api.github.com/users/alk224","html_url":"https://github.com/alk224","followers_url":"https://api.github.com/users/alk224/followers","following_url":"https://api.github.com/users/alk224/following{/other_user}","gists_url":"https://api.github.com/users/alk224/gists{/gist_id}","starred_url":"https://api.github.com/users/alk224/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alk224/subscriptions","organizations_url":"https://api.github.com/users/alk224/orgs","repos_url":"https://api.github.com/users/alk224/repos","events_url":"https://api.github.com/users/alk224/events{/privacy}","received_events_url":"https://api.github.com/users/alk224/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-03-20T19:33:04Z","updated_at":"2015-03-30T18:30:19Z","closed_at":null,"body":"usearch is frequently used for chimera checking, but due to the RAM limitation, only small data sets can be assessed, or else the data needs to be broken up into subsearches (my current approach).  vsearch uses the same published algorithm but with no limitations as it is open source.  I have compared the chimera filtering for a couple of small data sets and get identical results with either the qiime wrapper through identify_chimeric_seqs.py or vsearch run default.  Check it out at the link below.  Super useful.\r\n\r\nhttps://github.com/torognes/vsearch"},"comment":{"url":"https://api.github.com/repos/biocore/qiime/issues/comments/87781734","html_url":"https://github.com/biocore/qiime/issues/1962#issuecomment-87781734","issue_url":"https://api.github.com/repos/biocore/qiime/issues/1962","id":87781734,"user":{"login":"colinbrislawn","id":10355152,"avatar_url":"https://avatars.githubusercontent.com/u/10355152?v=3","gravatar_id":"","url":"https://api.github.com/users/colinbrislawn","html_url":"https://github.com/colinbrislawn","followers_url":"https://api.github.com/users/colinbrislawn/followers","following_url":"https://api.github.com/users/colinbrislawn/following{/other_user}","gists_url":"https://api.github.com/users/colinbrislawn/gists{/gist_id}","starred_url":"https://api.github.com/users/colinbrislawn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colinbrislawn/subscriptions","organizations_url":"https://api.github.com/users/colinbrislawn/orgs","repos_url":"https://api.github.com/users/colinbrislawn/repos","events_url":"https://api.github.com/users/colinbrislawn/events{/privacy}","received_events_url":"https://api.github.com/users/colinbrislawn/received_events","type":"User","site_admin":false},"created_at":"2015-03-30T18:30:19Z","updated_at":"2015-03-30T18:30:19Z","body":"@alk224\r\n>I wasn't sure if all the options would translate.\r\n\r\nBetter then translate! vsearch implements most of usearch 7 which is really elegant. Here is ref-based chimera checking. \r\n\r\n``` bash\r\n\r\nvsearch --uchime_ref centroids.mc2.fasta \\\r\n-db rdp_gold.fa \\\r\n--nonchimeras centroids.nochimeras.mc2.fasta\r\n\t### 1 min, ram = almost none\r\n```\r\n\r\nI'm really excited by the software @torognes and @frederic-mahe are developing. "}}