{"id":"W3010317290","doi":"10.1101/2020.03.02.973750","title":"Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"","keywords":"Reference genome; Computer science; Population; Contig; Genotyping; Data mining; Genome; Computational biology; Biology; Genetics; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.005564698,0.001210272,0.001052667,0.001066318,0.0006852036,0.002072401,0.002912873,0.002050657,0.005000225],"category_scores_gemma":[0.0085612,0.0007358792,0.001469078,0.001239285,0.000985156,0.002069261,0.002143197,0.002285623,0.004774159],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005906085,"about_ca_system_score_gemma":0.0007622379,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001328967,"about_ca_topic_score_gemma":0.001849622,"domain_scores_codex":[0.9952368,0.001358145,0.0005054684,0.001203146,0.001456611,0.0002399583],"domain_scores_gemma":[0.9923887,0.004303727,0.0006348274,0.001756398,0.0006507122,0.0002657241],"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":[0.002667754,0.0004867837,0.009550173,0.0009346579,0.0003341642,0.001561893,0.0008690987,0.01708238,0.7774543,0.01137576,0.01611389,0.161569],"study_design_scores_gemma":[0.0001470426,0.0005484326,0.003514549,0.00006717887,0.00005630552,0.001278972,0.0002352657,0.2388644,0.7258036,0.006749433,0.02249831,0.0002366126],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.155671,0.0008156154,0.7703546,0.00101566,0.0003883163,0.0003065253,0.005649304,0.06016683,0.005632205],"genre_scores_gemma":[0.2569719,0.0002519395,0.7257176,0.001243963,0.00009372656,0.0004775464,0.006727728,0.005027977,0.003487684],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005564698,"threshold_uncertainty_score":0.02942932,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03179059470450318,"score_gpt":0.2351160422038328,"score_spread":0.2033254474993296,"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."}}