{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/5","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/5/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/5/events","html_url":"https://github.com/PacificBiosciences/FALCON-pbsmrtpipe/issues/5","id":113883943,"number":5,"title":"SMRTLink GUI options for Polished HGAP 4 Assembly need some work","user":{"login":"ben-lerch","id":12494820,"avatar_url":"https://avatars.githubusercontent.com/u/12494820?v=3","gravatar_id":"","url":"https://api.github.com/users/ben-lerch","html_url":"https://github.com/ben-lerch","followers_url":"https://api.github.com/users/ben-lerch/followers","following_url":"https://api.github.com/users/ben-lerch/following{/other_user}","gists_url":"https://api.github.com/users/ben-lerch/gists{/gist_id}","starred_url":"https://api.github.com/users/ben-lerch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ben-lerch/subscriptions","organizations_url":"https://api.github.com/users/ben-lerch/orgs","repos_url":"https://api.github.com/users/ben-lerch/repos","events_url":"https://api.github.com/users/ben-lerch/events{/privacy}","received_events_url":"https://api.github.com/users/ben-lerch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-28T17:59:23Z","updated_at":"2015-10-28T18:14:04Z","closed_at":null,"body":"I have made some suggestions to the options I pulled from the GUI on Monday. They fall into 4 categories: looks good, possibly remove, revised, and possibly replace with multiple options. The last category is for options that appear to have multiple relevant parameters and should be broken up for the GUI. The possibly remove category is for options that don't appear relevant for the GUI. These are mostly ones concerning how jobs are managed on the cluster. I'm guessing the user won't have control of that, but I could be wrong. And for the revised category, I put the revised name and description just below the original option.\r\n\r\n#looks good\r\nMin. accuracy\r\nMinimum required alignment accuracy (percent)\r\n \r\n#possibly remove\r\nOption input_fofn\r\nOption input_fofn description\r\n \r\n#looks good\r\nMinimum confidence\r\nThe minimum confidence for a variant call to be output to variants.gff\r\n \r\n#revised\r\nOption length_cutoff_pr\r\nOption length_cutoff_pr description\r\nRead length cutoff (alignment stage)\r\nSpecifies the minimum read length used during the assembly stage\r\n \r\n#possibly remove\r\nOption pa_concurrent_jobs\r\nOption pa_concurrent_jobs description\r\n \r\n#looks good\r\nConcordant alignment\r\nMap subreads of a ZMW to the same genomic location\r\n \r\n#possibly remove\r\nOption input_type\r\nOption input_type description\r\n \r\n#possibly remove\r\nOption sge_option_da\r\nOption sge_option_da description\r\n \r\n#revised\r\nOption overlap_filtering_setting\r\nOption overlap_filtering_setting description\r\nMax overlap reported\r\nControls the maximum overlap reported for each read during overlap filtering.\r\n\r\n#revised\r\nOption ovlp_DBsplit_option\r\nOption ovlp_DBsplit_option description\r\nDataset Chunking (Overlapping detection of the error corrected reads)\r\nDetermines how to break the database into chunks that will be processed in parallel in the Overlapping detection of the error corrected reads stage. See for details: https://dazzlerblog.wordpress.com/2014/06/01/the-dazzler-db/#DBsplit\r\n\r\n#revised\r\nOption pa_DBsplit_option\r\nOption pa_DBsplit_option description\r\nDataset Chunking (Pre-assembly and error correction) \r\nDetermines how to break the database into chunks that will be processed in parallel in the Pre-assembly and error correction stage. See for details: https://dazzlerblog.wordpress.com/2014/06/01/the-dazzler-db/#DBsplit\r\n\r\n#possibly remove\r\nParameter spec\r\nParameter spec\r\n \r\n#possibly remove\r\nOption sge_option_pla\r\nOption sge_option_pla description\r\n\r\n#possibly remove \r\nOption jobqueue\r\nOption jobqueue description\r\n \r\n#looks good\r\nDiploid mode (experimental)\r\nEnable detection of heterozygous variants (experimental)\r\n \r\n#looks good\r\nMin. length\r\nMinimum required alignment length\r\n \r\n#possibly remove\r\nOption sge_option_cns\r\nOption sge_option_cns description\r\n \r\n#possibly replace with multiple options\r\nOption pa_HPCdaligner_option\r\nOption pa_HPCdaligner_option description\r\n\r\n#possibly replace with multiple options\r\nOption falcon_sense_option\r\nOption falcon_sense_option description\r\n\r\n #possibly remove\r\nOption sge_option_fc\r\nOption sge_option_fc description\r\n \r\n#possibly remove\r\nOption job_type\r\nOption job_type description\r\n \r\n#possibly remove\r\nOption sge_option_la\r\nOption sge_option_la description\r\n \r\n#looks good\r\nUse CCS\r\nMap the ccsSequence to the genome first, then align subreads to the interval that the CCS reads mapped to. useccs: only maps subreads that span the length of the template. useccsall: maps all subreads. useccsdenovo: maps ccs only.\r\n \r\n#revised\r\nAlgorithm\r\nAlgorithm name\r\nAlgorithm\r\nSpecify whether to use Quiver or Plurality \r\n\r\n#looks good\r\nMinimum coverage\r\nThe minimum site coverage that must be achieved for variant calls and consensus to be calculated for a site.\r\n \r\n#possibly remove\r\nOption sge_option_pda\r\nOption sge_option_pda description\r\n \r\n#looks good\r\nHit policy\r\nSpecify a policy for how to treat multiple hit random : selects a random hit. all : selects all hits. allbest : selects all the best score hits. randombest: selects a random hit from all best score hits. leftmost : selects a hit which has the best score and the smallest mapping coordinate in any reference. Default value is randombest.\r\n \r\n#possibly replace with multiple options\r\nOption ovlp_HPCdaligner_option\r\nOption ovlp_HPCdaligner_option description\r\n \r\n#revised\r\nOption length_cutoff\r\nOption length_cutoff description\r\nRead length cutoff (error correction stage)\r\nSpecifies the minimum read length used during the error correction stage\r\n\r\nAlgorithm options\r\nList of space-separated arguments passed to BLASR (etc.)\r\n\r\n#possibly remove \r\nOption ovlp_concurrent_jobs\r\nOption ovlp_concurrent_jobs description\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/comments/151938681","html_url":"https://github.com/PacificBiosciences/FALCON-pbsmrtpipe/issues/5#issuecomment-151938681","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON-pbsmrtpipe/issues/5","id":151938681,"user":{"login":"ben-lerch","id":12494820,"avatar_url":"https://avatars.githubusercontent.com/u/12494820?v=3","gravatar_id":"","url":"https://api.github.com/users/ben-lerch","html_url":"https://github.com/ben-lerch","followers_url":"https://api.github.com/users/ben-lerch/followers","following_url":"https://api.github.com/users/ben-lerch/following{/other_user}","gists_url":"https://api.github.com/users/ben-lerch/gists{/gist_id}","starred_url":"https://api.github.com/users/ben-lerch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ben-lerch/subscriptions","organizations_url":"https://api.github.com/users/ben-lerch/orgs","repos_url":"https://api.github.com/users/ben-lerch/repos","events_url":"https://api.github.com/users/ben-lerch/events{/privacy}","received_events_url":"https://api.github.com/users/ben-lerch/received_events","type":"User","site_admin":false},"created_at":"2015-10-28T18:14:04Z","updated_at":"2015-10-28T18:14:04Z","body":"OK, and I noticed I didn't comment on the Algorithms Options option. Here is my suggestion:\r\n\r\n#revised\r\nAlgorithm options\r\nList of space-separated arguments passed to BLASR (etc.)\r\nBLASR options\r\nList of space-separated arguments passed to BLASR. See BLASR documentation for full list of options. Basic options are: -useQuality -minMatch -bestn -minPctSimilarity\r\n\r\nThen link to this somewhere:\r\n-useQuality\r\n               Use substitution/insertion/deletion/merge quality values to score gap and\r\n               mismatch penalties in pairwise alignments.  Because the insertion and deletion\r\n               rates are much higher than substitution, this will make many alignments\r\n               favor an insertion/deletion over a substitution.  Naive consensus calling methods\r\n               will then often miss substitution polymorphisms. This option should be\r\n               used when calling consensus using the Quiver method.  Furthermore, when\r\n               not using quality values to score alignments, there will be a lower consensus\r\n               accuracy in homopolymer regions.\r\n\r\n -minMatch\r\n               Minimum seed length.  Higher minMatch will speed up alignment, but decrease sensitivity.\r\n\r\n -bestn\r\n               Report the top 'n' alignments.\r\n\r\n -minPctSimilarity\r\n               Report alignments only if their percentage similarity is greater than minPctSimilarity.\r\n"}}