{"id":"W4286820170","doi":"10.1101/2022.06.21.497051","title":"Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies’ MinION device","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Nanopore and Nanochannel Transport Studies","field":"Engineering","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Burnaby Hospital; Simon Fraser University; University of British Columbia; Canada's Michael Smith Genome Sciences Centre","funders":"","keywords":"Plasmid; Minion; Nanopore sequencing; Sanger sequencing; Biology; DNA sequencing; Computational biology; Consensus sequence; Sequence (biology); Genetics; Computer science; DNA; Base sequence","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":[0.002084937,0.0009140426,0.0008615628,0.001087964,0.0005975811,0.000720757,0.0008584866,0.0009256341,0.00415822],"category_scores_gemma":[0.00397277,0.0006785894,0.0006073774,0.0004857219,0.0005278856,0.0008750165,0.0009314292,0.0009536829,0.004097395],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005128085,"about_ca_system_score_gemma":0.001098265,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009093644,"about_ca_topic_score_gemma":0.001611985,"domain_scores_codex":[0.9970775,0.0005873795,0.0003274913,0.0006346364,0.00115945,0.0002135285],"domain_scores_gemma":[0.9970279,0.0009719826,0.000397409,0.0005709924,0.0008443483,0.0001872792],"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":[0.0001180729,0.00003539705,0.0006973271,0.0002405996,0.00001698476,0.0001034429,0.000118267,0.000294765,0.9755078,0.0008619319,0.001183479,0.02082207],"study_design_scores_gemma":[0.00001039578,0.0001241587,0.001404651,0.00003334591,0.00001544056,0.0003322039,0.00002394596,0.003346223,0.9831542,0.0002019318,0.01132694,0.00002641484],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1994362,0.001763318,0.7754945,0.0004340223,0.0002574699,0.001122185,0.005770156,0.009718885,0.006003324],"genre_scores_gemma":[0.2602905,0.001434312,0.7119805,0.0004059732,0.00005383754,0.001377705,0.01409773,0.001515425,0.008844011],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.00415822,"threshold_uncertainty_score":0.01391065,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03812013100522212,"score_gpt":0.2337582221709368,"score_spread":0.1956380911657146,"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."}}