{"action":"opened","issue":{"url":"https://api.github.com/repos/torognes/vsearch/issues/309","repository_url":"https://api.github.com/repos/torognes/vsearch","labels_url":"https://api.github.com/repos/torognes/vsearch/issues/309/labels{/name}","comments_url":"https://api.github.com/repos/torognes/vsearch/issues/309/comments","events_url":"https://api.github.com/repos/torognes/vsearch/issues/309/events","html_url":"https://github.com/torognes/vsearch/issues/309","id":324538772,"number":309,"title":"fastq_pctid option for fastq_mergepairs","user":{"login":"pschloss","id":1264132,"avatar_url":"https://avatars0.githubusercontent.com/u/1264132?v=4","gravatar_id":"","url":"https://api.github.com/users/pschloss","html_url":"https://github.com/pschloss","followers_url":"https://api.github.com/users/pschloss/followers","following_url":"https://api.github.com/users/pschloss/following{/other_user}","gists_url":"https://api.github.com/users/pschloss/gists{/gist_id}","starred_url":"https://api.github.com/users/pschloss/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pschloss/subscriptions","organizations_url":"https://api.github.com/users/pschloss/orgs","repos_url":"https://api.github.com/users/pschloss/repos","events_url":"https://api.github.com/users/pschloss/events{/privacy}","received_events_url":"https://api.github.com/users/pschloss/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-18T20:15:47Z","updated_at":"2018-05-18T20:15:47Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"I'm trying to replicate read pair assembly that I've tested with `usearch` and want to replicate with `vsearch`. In the [`usearch`](https://www.drive5.com/usearch/manual/merge_options.html) documentation, it suggests raising `fastq_pctid` and `fastq_maxdiffs` from the default values of 90% and 5, respectively, as the amount of overlap between the reads increases. `vsearch` has `fastq_maxdiffs`, which defaults to 10 and `fastq_maxdiffpct` defaults to 100%. I think fastq_maxdiffpct is one minus `usearch`'s `fastq_pctid` value. Is that right?\r\n\r\nAlso, from your documentation it sounds like you're saying that `fastq_maxdiffpct` is superfluous:\r\n\r\n> There are other more sophisticated rules in the merging algorithm that will discard read pairs with a high fraction of mismatches\r\n\r\nWhat are you all counting as those \"more sophisticated rules\"?"}}
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