{"action":"created","issue":{"url":"https://api.github.com/repos/bioboxes/rfc/issues/183","labels_url":"https://api.github.com/repos/bioboxes/rfc/issues/183/labels{/name}","comments_url":"https://api.github.com/repos/bioboxes/rfc/issues/183/comments","events_url":"https://api.github.com/repos/bioboxes/rfc/issues/183/events","html_url":"https://github.com/bioboxes/rfc/issues/183","id":113900469,"number":183,"title":"Read based Assembly Evaluation","user":{"login":"pbelmann","id":8780236,"avatar_url":"https://avatars.githubusercontent.com/u/8780236?v=3","gravatar_id":"","url":"https://api.github.com/users/pbelmann","html_url":"https://github.com/pbelmann","followers_url":"https://api.github.com/users/pbelmann/followers","following_url":"https://api.github.com/users/pbelmann/following{/other_user}","gists_url":"https://api.github.com/users/pbelmann/gists{/gist_id}","starred_url":"https://api.github.com/users/pbelmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbelmann/subscriptions","organizations_url":"https://api.github.com/users/pbelmann/orgs","repos_url":"https://api.github.com/users/pbelmann/repos","events_url":"https://api.github.com/users/pbelmann/events{/privacy}","received_events_url":"https://api.github.com/users/pbelmann/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/bioboxes/rfc/labels/A-RFCs","name":"A-RFCs","color":"bfd4f2"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-10-28T19:10:29Z","updated_at":"2015-11-02T08:28:26Z","closed_at":null,"body":"Besides our current (reference based and reference free) assembly benchmark interface, there is a way to evaluate assemblies based on the initial reads data.\r\nBioboxes should provide an interface for these kind of tools.\r\n\r\nThis issue should be closed when there is\r\n\r\n  * A read based assembly benchmark rfc.\r\n\r\n  * A schema.\r\n\r\n  * A verify command for testing read based assembly benchmark bioboxes.\r\n\r\n  * At least one example implementing the interface.\r\n\r\n\r\nCurrent Examples:\r\n\r\n* (ALE)[https://github.com/AlphaSquad/ALE] Biobox (work in progress) \r\n\r\n* (VALET)[https://github.com/AlphaSquad/VALET] Biobox (work in progress) \r\n\r\nCurrent RFC: https://github.com/pbelmann/rfc/blob/pbelmann-read-based-assembly-evaluation/container/assembly-evaluation/read-based-assembly-evaluation/rfc.mkd\r\n"},"comment":{"url":"https://api.github.com/repos/bioboxes/rfc/issues/comments/152950149","html_url":"https://github.com/bioboxes/rfc/issues/183#issuecomment-152950149","issue_url":"https://api.github.com/repos/bioboxes/rfc/issues/183","id":152950149,"user":{"login":"pbelmann","id":8780236,"avatar_url":"https://avatars.githubusercontent.com/u/8780236?v=3","gravatar_id":"","url":"https://api.github.com/users/pbelmann","html_url":"https://github.com/pbelmann","followers_url":"https://api.github.com/users/pbelmann/followers","following_url":"https://api.github.com/users/pbelmann/following{/other_user}","gists_url":"https://api.github.com/users/pbelmann/gists{/gist_id}","starred_url":"https://api.github.com/users/pbelmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbelmann/subscriptions","organizations_url":"https://api.github.com/users/pbelmann/orgs","repos_url":"https://api.github.com/users/pbelmann/repos","events_url":"https://api.github.com/users/pbelmann/events{/privacy}","received_events_url":"https://api.github.com/users/pbelmann/received_events","type":"User","site_admin":false},"created_at":"2015-11-02T08:28:26Z","updated_at":"2015-11-02T08:28:26Z","body":"> This is a good idea, I would use this in combination with the existing reference based biobox to examine assemblies. I noticed you checked into the CLI an assembly fasta file but not not any reads. Is this an assembly of the existing genome paired reads fastq file.\r\n\r\nThis reads https://github.com/bioboxes/command-line-interface/blob/release/0.3.0/biobox_cli/verification/data/genome_paired_reads.fq.gz\r\n\r\nand this assembly https://github.com/bioboxes/command-line-interface/blob/release/0.3.0/biobox_cli/verification/data/read_based_benchmark/assembly.fasta\r\n\r\nare used for verification. \r\n\r\n> I have changed lib1 to ray as I believe the RFC indicates the IDs should match. Is this correct? Also I believe the reads should also be a list.\r\n\r\nYes we could specify it as list. Maybe @AlphaSquad (Adrian) has an opinion to this, since he is implementing ALE and VALET with this interface.\r\n\r\n> A fasta A must have a corresponding fastq A for evaluation? Or is it the case that all reads will be evaluated against all assemblies?\r\n\r\nAll reads against all assemblies. (Same as quast)\r\n\r\n~~~\r\n[fasta A], [fastq A] -> evaluation C\r\n~~~"}}