{"id":"W3200050118","doi":"10.1099/mgen.0.000651","title":"Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Genotyping; Computational biology; SNP; Genome; Biology; SNP genotyping; Whole genome sequencing; Population; Genetics; Genotype; Single-nucleotide polymorphism; Gene; Medicine","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":[0.002624643,0.0007949774,0.0008351568,0.002041781,0.0005988646,0.001693887,0.00120711,0.001198991,0.004503185],"category_scores_gemma":[0.004748385,0.0006695087,0.0008067584,0.0015154,0.0006296425,0.001175689,0.001517808,0.0008519142,0.003735434],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004697458,"about_ca_system_score_gemma":0.0007659143,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001110068,"about_ca_topic_score_gemma":0.003197566,"domain_scores_codex":[0.9968863,0.0006827621,0.0002754828,0.00105852,0.0008907955,0.0002061206],"domain_scores_gemma":[0.9959339,0.001761535,0.0008473934,0.0008848077,0.0004310954,0.0001412691],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001882174,0.0003033502,0.03394122,0.0009830934,0.0003752477,0.0004895033,0.001117488,0.01740883,0.6589329,0.005610417,0.01313454,0.2658213],"study_design_scores_gemma":[0.000146239,0.0006011192,0.04835206,0.0001347426,0.0001842899,0.001034214,0.0003958323,0.1824329,0.7172928,0.004118211,0.04490479,0.0004027841],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.4165568,0.001396122,0.5141013,0.0004742339,0.0003179828,0.0005169893,0.01674204,0.03953126,0.01036329],"genre_scores_gemma":[0.2222649,0.0003145072,0.7603756,0.0003144064,0.00004040882,0.0005844152,0.009563225,0.001144473,0.005398139],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.004503185,"threshold_uncertainty_score":0.01506466,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01342286083316546,"score_gpt":0.2086689526788758,"score_spread":0.1952460918457103,"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."}}