{"id":"W4401537043","doi":"10.3390/v16081293","title":"A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome","year":2024,"lang":"en","type":"article","venue":"Viruses","topic":"Animal Disease Management and Epidemiology","field":"Agricultural and Biological Sciences","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency","funders":"Oak Ridge Institute for Science and Education; Oak Ridge Associated Universities; U.S. Department of Agriculture; U.S. Department of Energy","keywords":"Annotation; Genome; Pipeline (software); African swine fever virus; Sequence assembly; Reference genome; Outbreak; Computational biology; DNA sequencing; Whole genome sequencing; Computer science; Biology; Genetics; Virus; Virology; DNA; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000218873,0.0000729588,0.000146539,0.00001599793,0.00005058399,0.00002700232,0.0000569304,0.00003222904,0.0001290076],"category_scores_gemma":[0.00008100062,0.00002771749,0.00005514838,0.0001390051,0.0000402523,0.00009360801,0.00003386492,0.00002360958,0.000008055797],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007145632,"about_ca_system_score_gemma":0.000003970283,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001406265,"about_ca_topic_score_gemma":0.0001157327,"domain_scores_codex":[0.9994528,0.00003203464,0.0001561077,0.0001720774,0.00006328286,0.0001236975],"domain_scores_gemma":[0.99963,0.0002430814,0.00003601109,0.0000205765,0.0000316719,0.00003870828],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003072227,0.00004399,0.001644925,0.00008045801,0.00004996877,0.000003238927,0.00007741192,0.000005722629,0.9315164,0.005590352,0.007640211,0.05304009],"study_design_scores_gemma":[0.0003815713,0.0005774066,0.2397473,0.00004076281,0.0001233471,0.000001241307,0.0003030701,0.002792142,0.004152724,0.008895868,0.7426898,0.0002947932],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9954209,0.001973889,0.0005077377,0.0008941225,0.0000560817,0.0002069641,0.0004308812,0.00006338985,0.0004460092],"genre_scores_gemma":[0.9987934,0.0002102869,0.0001590846,0.0003940916,0.0001597241,0.00001976699,0.00005491942,9.523449e-7,0.0002077638],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9273637,"threshold_uncertainty_score":0.1412542,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05077980021641147,"score_gpt":0.2934292686659484,"score_spread":0.2426494684495369,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}