{"id":"W4220954508","doi":"10.1101/2022.03.04.22271870","title":"Nanopore sequencing for <i>Mycobacterium tuberculosis</i> drug susceptibility testing and outbreak investigation","year":2022,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier de l’Université de Montréal","funders":"Vlaamse regering; Fonds Wetenschappelijk Onderzoek; National Research Foundation; National Science Foundation; Translational Genomics Research Institute; International Seafood Sustainability Foundation; Wellcome Trust; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Carnegie Corporation of New York","keywords":"Nanopore sequencing; Genotyping; Indel; Single-nucleotide polymorphism; Genetics; Biology; Minion; Computational biology; Illumina dye sequencing; Whole genome sequencing; Nanopore; DNA sequencing; Genotype; Genome; Gene; Nanotechnology","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006184687,0.0002996472,0.0003316585,0.0008482533,0.0004142369,0.0008093424,0.0004257723,0.0004746094,0.003442865],"category_scores_gemma":[0.00175565,0.0001828547,0.0002996906,0.00072265,0.0002447158,0.0003442698,0.0007154492,0.0002759918,0.001011441],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005077324,"about_ca_system_score_gemma":0.0004486236,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006605577,"about_ca_topic_score_gemma":0.01248263,"domain_scores_codex":[0.9993213,0.0001585675,0.00005284576,0.0002425553,0.0001523948,0.00007229458],"domain_scores_gemma":[0.9987619,0.0003804212,0.0003547623,0.0001562212,0.0002471363,0.00009947048],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007923284,0.0001084642,0.4449139,0.001007888,0.0002435882,0.00106375,0.001021105,0.006329334,0.3904339,0.001216962,0.008482296,0.1443866],"study_design_scores_gemma":[0.00003517634,0.0003332013,0.7362707,0.000373225,0.0002590424,0.002255431,0.001063306,0.02645241,0.1825005,0.002070612,0.04829701,0.00008937628],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9303356,0.001601557,0.04549545,0.0006373654,0.00006534718,0.0002050091,0.01078297,0.001324952,0.00955177],"genre_scores_gemma":[0.9297672,0.000417812,0.05915079,0.000517343,0.00003576454,0.0001441509,0.007941048,0.0001923443,0.0018335],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006605577,"threshold_uncertainty_score":0.01313424,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06532132765454551,"score_gpt":0.3255585056833978,"score_spread":0.2602371780288523,"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."}}