{"id":"W4391805795","doi":"10.1139/cjm-2023-0175","title":"Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies","year":2024,"lang":"en","type":"article","venue":"Canadian Journal of Microbiology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":52,"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; Genome; Computational biology; Biology; Whole genome sequencing; Minion; Sequence assembly; DNA sequencing; Genetics; Computer science; Gene; Single-nucleotide polymorphism; Genotype","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":true,"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":[0.0005380478,0.000218542,0.0003404403,0.0001507532,0.0001905013,0.0001408197,0.0005762191,0.0002113428,0.00003838159],"category_scores_gemma":[0.0002066425,0.0001537283,0.0001089463,0.0001025901,0.0005916581,0.000009394415,0.000231514,0.0001916589,0.000001819156],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003600357,"about_ca_system_score_gemma":0.0006652228,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006964389,"about_ca_topic_score_gemma":0.0005876642,"domain_scores_codex":[0.9987118,0.0001227989,0.0003980906,0.0003601614,0.00003049101,0.0003767211],"domain_scores_gemma":[0.9990762,0.0001496986,0.0001968689,0.0003590399,0.0001168599,0.0001013569],"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":[0.00006794831,0.000003096185,0.00006969109,0.00005766105,0.0003303245,0.00001325089,0.0009986432,0.0000639148,0.9778184,0.00004521895,0.005610026,0.01492188],"study_design_scores_gemma":[0.001666606,0.001235851,0.0001461077,0.0001966264,0.0002519718,0.0008467737,0.008338789,0.0006895526,0.1643425,0.002300614,0.8194542,0.0005304528],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9019603,0.09085093,0.0001353908,0.003923655,0.0007302105,0.000425516,0.001883734,0.000007851798,0.00008237206],"genre_scores_gemma":[0.9839485,0.007236285,0.007908798,0.0002059381,0.0002646863,0.00001701414,0.0001733223,0.00003837284,0.0002070863],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8138441,"threshold_uncertainty_score":0.6268857,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02468867088896726,"score_gpt":0.2425766196878419,"score_spread":0.2178879487988747,"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."}}