{"id":"W4387058463","doi":"10.1101/2023.09.25.559359","title":"Do we still need Illumina sequencing data?: Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and v14 library prep kits for Gram negative bacteria whole genome assemblies","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada","keywords":"Nanopore sequencing; Illumina dye sequencing; Indel; Minion; Computational biology; Genome; Computer science; Whole genome sequencing; Biology; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.01857438,0.0009055695,0.0006507864,0.0007229528,0.0005799756,0.002148644,0.001440406,0.001189994,0.003548726],"category_scores_gemma":[0.01301596,0.0004807319,0.0006537679,0.000825269,0.0003608731,0.001726147,0.0009011165,0.0005386434,0.001580752],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001584462,"about_ca_system_score_gemma":0.001817312,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008928523,"about_ca_topic_score_gemma":0.03159428,"domain_scores_codex":[0.9921235,0.003300466,0.0005220412,0.0007109056,0.002879594,0.0004633404],"domain_scores_gemma":[0.9906896,0.003335842,0.0007359722,0.000339141,0.003827052,0.001072336],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003906955,0.0007567152,0.04131015,0.006502083,0.0007229343,0.0005101757,0.0009302583,0.03406219,0.2863896,0.004635589,0.04226971,0.5780038],"study_design_scores_gemma":[0.0004900595,0.008919482,0.08931372,0.002026399,0.0008467202,0.001043947,0.002217909,0.1465572,0.5576833,0.00368803,0.1866432,0.0005700637],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6021017,0.03934066,0.2867491,0.01279372,0.0009845095,0.002278344,0.01669563,0.008914968,0.03014135],"genre_scores_gemma":[0.3420772,0.01014948,0.6180966,0.002054738,0.0001274999,0.0006757133,0.01853673,0.002006906,0.006275007],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01857438,"threshold_uncertainty_score":0.09823185,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0409358608711446,"score_gpt":0.2574024657363673,"score_spread":0.2164666048652227,"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."}}